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Dougan KE, Bellantuono AJ, Kahlke T, Abbriano RM, Chen Y, Shah S, Granados-Cifuentes C, van Oppen MJH, Bhattacharya D, Suggett DJ, Rodriguez-Lanetty M, Chan CX. Whole-genome duplication in an algal symbiont bolsters coral heat tolerance. SCIENCE ADVANCES 2024; 10:eadn2218. [PMID: 39028812 PMCID: PMC11259175 DOI: 10.1126/sciadv.adn2218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
The algal endosymbiont Durusdinium trenchii enhances the resilience of coral reefs under thermal stress. D. trenchii can live freely or in endosymbiosis, and the analysis of genetic markers suggests that this species has undergone whole-genome duplication (WGD). However, the evolutionary mechanisms that underpin the thermotolerance of this species are largely unknown. Here, we present genome assemblies for two D. trenchii isolates, confirm WGD in these taxa, and examine how selection has shaped the duplicated genome regions using gene expression data. We assess how the free-living versus endosymbiotic lifestyles have contributed to the retention and divergence of duplicated genes, and how these processes have enhanced the thermotolerance of D. trenchii. Our combined results suggest that lifestyle is the driver of post-WGD evolution in D. trenchii, with the free-living phase being the most important, followed by endosymbiosis. Adaptations to both lifestyles likely enabled D. trenchii to provide enhanced thermal stress protection to the host coral.
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Affiliation(s)
- Katherine E. Dougan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yibi Chen
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sarah Shah
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Camila Granados-Cifuentes
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Madeleine J. H. van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - David J. Suggett
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Mauricio Rodriguez-Lanetty
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
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2
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Fu D, Weng X, Su Y, Hong B, Zhao A, Lin J. Establishing a model composed of immune-related gene-modules to predict tumor immunotherapy response. Sci Rep 2024; 14:16630. [PMID: 39025898 PMCID: PMC11258235 DOI: 10.1038/s41598-024-67742-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024] Open
Abstract
At present, tumor immunotherapy has been widely applied to treat various cancers. However, the accuracy of predicting treatment efficacy has not yet achieved a significant breakthrough. This study aimed to construct a prediction model based on the modified WGCNA algorithm to precisely judge the anti-tumor immune response. First, we used a murine colon cancer model to screen corresponding DEGs according to different groups. GSEA was used to analyze the potential mechanisms of the immune-related DEGs (irDEGs) in each group. Subsequently, the intersection of the irDEGs in every group was acquired, and 7 gene-modules were mapped. Finally, 4 gene-modules including cogenes, antiPD-1 immu-genes, chemo immu-genes and comb immu-genes, were selected for subsequent study. Furthermore, a clinical dataset of gastric cancer patients receiving immunotherapy was enrolled, and the irDEGs were identified. A total of 34 vital irDEGs were obtained from the intersections of the vital irDEGs and the four gene-modules. Next, the vital irDEGs were analyzed by the modified WGCNA algorithm, and the correlation coefficients between the 4 gene-modules and the response status to immunotherapy were calculated. Thus, a prediction model based on correlation coefficients was built, and the corresponding model scores were acquired. The AUC calculated according to the model score was 0.727, which was non-inferior to that of the ESTIMATE score and the TIDE score. Meanwhile, the AUC calculated according to the classification of the model scores was 0.705, which was non-inferior to that of the ESTIMATE classification and the TIDE classification. The prediction accuracy of the model was validated in clinical datasets of other cancers.
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Affiliation(s)
- Deqiang Fu
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Xiaoyuan Weng
- Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Quanzhou Medical College, Quanzhou, China
| | - Yunxia Su
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Binhuang Hong
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Aiyue Zhao
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
| | - Jianqing Lin
- Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
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Zhang W, Higgins EE, Robinson SJ, Clarke WE, Boyle K, Sharpe AG, Fobert PR, Parkin IAP. A systems genomics and genetics approach to identify the genetic regulatory network for lignin content in Brassica napus seeds. FRONTIERS IN PLANT SCIENCE 2024; 15:1393621. [PMID: 38903439 PMCID: PMC11188405 DOI: 10.3389/fpls.2024.1393621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/29/2024] [Indexed: 06/22/2024]
Abstract
Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eighty-three subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality.
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Affiliation(s)
- Wentao Zhang
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Erin E. Higgins
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Stephen J. Robinson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Wayne E. Clarke
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Kerry Boyle
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
| | - Pierre R. Fobert
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, ON, Canada
| | - Isobel A. P. Parkin
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
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de los Cobos FP, García-Gómez BE, Orduña-Rubio L, Batlle I, Arús P, Matus JT, Eduardo I. Exploring large-scale gene coexpression networks in peach ( Prunus persica L.): a new tool for predicting gene function. HORTICULTURE RESEARCH 2024; 11:uhad294. [PMID: 38487296 PMCID: PMC10939413 DOI: 10.1093/hr/uhad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/17/2023] [Indexed: 03/17/2024]
Abstract
Peach is a model for Prunus genetics and genomics, however, identifying and validating genes associated to peach breeding traits is a complex task. A gene coexpression network (GCN) capable of capturing stable gene-gene relationships would help researchers overcome the intrinsic limitations of peach genetics and genomics approaches and outline future research opportunities. In this study, we created four GCNs from 604 Illumina RNA-Seq libraries. We evaluated the performance of every GCN in predicting functional annotations using an algorithm based on the 'guilty-by-association' principle. The GCN with the best performance was COO300, encompassing 21 956 genes. To validate its performance predicting gene function, we performed two case studies. In case study 1, we used two genes involved in fruit flesh softening: the endopolygalacturonases PpPG21 and PpPG22. Genes coexpressing with both genes were extracted and referred to as melting flesh (MF) network. Finally, we performed an enrichment analysis of MF network and compared the results with the current knowledge regarding peach fruit softening. The MF network mostly included genes involved in cell wall expansion and remodeling, and with expressions triggered by ripening-related phytohormones, such as ethylene, auxin, and methyl jasmonate. In case study 2, we explored potential targets of the anthocyanin regulator PpMYB10.1 by comparing its gene-centered coexpression network with that of its grapevine orthologues, identifying a common regulatory network. These results validated COO300 as a powerful tool for peach and Prunus research. This network, renamed as PeachGCN v1.0, and the scripts required to perform a function prediction analysis are available at https://github.com/felipecobos/PeachGCN.
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Affiliation(s)
- Felipe Pérez de los Cobos
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA) , Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Beatriz E García-Gómez
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Luis Orduña-Rubio
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, 46908, Valencia, Spain
| | - Ignasi Batlle
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA) , Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
| | - Pere Arús
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, 46908, Valencia, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Lei W, Zhu H, Cao M, Zhang F, Lai Q, Lu S, Dong W, Sun J, Ru D. From genomics to metabolomics: Deciphering sanguinarine biosynthesis in Dicranostigma leptopodum. Int J Biol Macromol 2024; 257:128727. [PMID: 38092109 DOI: 10.1016/j.ijbiomac.2023.128727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/15/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023]
Abstract
Dicranostigma leptopodum (Maxim) Fedde (DLF) is a renowned medicinal plant in China, known to be rich in alkaloids. However, the unavailability of a reference genome has impeded investigation into its plant metabolism and genetic breeding potential. Here we present a high-quality chromosomal-level genome assembly for DLF, derived using a combination of Nanopore long-read sequencing, Illumina short-read sequencing and Hi-C technologies. Our assembly genome spans a size of 621.81 Mb with an impressive contig N50 of 93.04 Mb. We show that the species-specific whole-genome duplication (WGD) of DLF and Papaver somniferum corresponded to two rounds of WGDs of Papaver setigerum. Furthermore, we integrated comprehensive homology searching, gene family analyses and construction of a gene-to-metabolite network. These efforts led to the discovery of co-expressed transcription factors, including NAC and bZIP, alongside sanguinarine (SAN) pathway genes CYP719 (CFS and SPS). Notably, we identified P6H as a promising gene for enhancing SAN production. By providing the first reference genome for Dicranostigma, our study confirms the genomic underpinning of SAN biosynthesis and establishes a foundation for advancing functional genomic research on Papaveraceae species. Our findings underscore the pivotal role of high-quality genome assemblies in elucidating genetic variations underlying the evolutionary origin of secondary metabolites.
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Affiliation(s)
- Weixiao Lei
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Man Cao
- Gansu Pharmacovigilance Center, Lanzhou 730070, China
| | - Feng Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qing Lai
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shengming Lu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Wenpan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.
| | - Jiahui Sun
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China.
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De R, Whiteley M, Azad RK. A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1. mSystems 2023; 8:e0047323. [PMID: 37921470 PMCID: PMC10734507 DOI: 10.1128/msystems.00473-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE We present here a new systems-level approach to decipher genetic factors and biological pathways associated with virulence and/or antibiotic treatment of bacterial pathogens. The power of this approach was demonstrated by application to a well-studied pathogen Pseudomonas aeruginosa PAO1. Our gene co-expression network-based approach unraveled known and unknown genes and their networks associated with pathogenicity in P. aeruginosa PAO1. The systems-level investigation of P. aeruginosa PAO1 helped identify putative pathogenicity and resistance-associated genetic factors that could not otherwise be detected by conventional approaches of differential gene expression analysis. The network-based analysis uncovered modules that harbor genes not previously reported by several original studies on P. aeruginosa virulence and resistance. These could potentially act as molecular determinants of P. aeruginosa PAO1 pathogenicity and responses to antibiotics.
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Affiliation(s)
- Ronika De
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
| | - Marvin Whiteley
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
- Department of Mathematics, University of North Texas, Denton, Texas, USA
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7
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Trujillo-Ortíz R, Espinal-Enríquez J, Hernández-Lemus E. The Role of Transcription Factors in the Loss of Inter-Chromosomal Co-Expression for Breast Cancer Subtypes. Int J Mol Sci 2023; 24:17564. [PMID: 38139393 PMCID: PMC10743684 DOI: 10.3390/ijms242417564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Breast cancer encompasses a diverse array of subtypes, each exhibiting distinct clinical characteristics and treatment responses. Unraveling the underlying regulatory mechanisms that govern gene expression patterns in these subtypes is essential for advancing our understanding of breast cancer biology. Gene co-expression networks (GCNs) help us identify groups of genes that work in coordination. Previous research has revealed a marked reduction in the interaction of genes located on different chromosomes within GCNs for breast cancer, as well as for lung, kidney, and hematopoietic cancers. However, the reasons behind why genes on the same chromosome often co-express remain unclear. In this study, we investigate the role of transcription factors in shaping gene co-expression networks within the four main breast cancer subtypes: Luminal A, Luminal B, HER2+, and Basal, along with normal breast tissue. We identify communities within each GCN and calculate the transcription factors that may regulate these communities, comparing the results across different phenotypes. Our findings indicate that, in general, regulatory behavior is to a large extent similar among breast cancer molecular subtypes and even in healthy networks. This suggests that transcription factor motif usage does not fully determine long-range co-expression patterns. Specific transcription factor motifs, such as CCGGAAG, appear frequently across all phenotypes, even involving multiple highly connected transcription factors. Additionally, certain transcription factors exhibit unique actions in specific subtypes but with limited influence. Our research demonstrates that the loss of inter-chromosomal co-expression is not solely attributable to transcription factor regulation. Although the exact mechanism responsible for this phenomenon remains elusive, this work contributes to a better understanding of gene expression regulatory programs in breast cancer.
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Affiliation(s)
- Rodrigo Trujillo-Ortíz
- Computational Genomics Division, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City 01010, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City 01010, Mexico
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Sharma N, Madan B, Khan MS, Sandhu KS, Raghuram N. Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1135675. [PMID: 37351205 PMCID: PMC10282765 DOI: 10.3389/fpls.2023.1135675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 05/10/2023] [Indexed: 06/24/2023]
Abstract
Rice is an important target to improve crop nitrogen (N) use efficiency (NUE), and the identification and shortlisting of the candidate genes are still in progress. We analyzed data from 16 published N-responsive transcriptomes/microarrays to identify, eight datasets that contained the maximum number of 3020 common genes, referred to as N-responsive genes. These include different classes of transcription factors, transporters, miRNA targets, kinases and events of post-translational modifications. A Weighted gene co-expression network analysis (WGCNA) with all the 3020 N-responsive genes revealed 15 co-expression modules and their annotated biological roles. Protein-protein interaction network analysis of the main module revealed the hub genes and their functional annotation revealed their involvement in the ubiquitin process. Further, the occurrences of G-quadruplex sequences were examined, which are known to play important roles in epigenetic regulation but are hitherto unknown in N-response/NUE. Out of the 3020 N-responsive genes studied, 2298 contained G-quadruplex sequences. We compared these N-responsive genes containing G-quadruplex sequences with the 3601 genes we previously identified as NUE-related (for being both N-responsive and yield-associated). This analysis revealed 389 (17%) NUE-related genes containing G-quadruplex sequences. These genes may be involved in the epigenetic regulation of NUE, while the rest of the 83% (1811) genes may regulate NUE through genetic mechanisms and/or other epigenetic means besides G-quadruplexes. A few potentially important genes/processes identified as associated with NUE were experimentally validated in a pair of rice genotypes contrasting for NUE. The results from the WGCNA and G4 sequence analysis of N-responsive genes helped identify and shortlist six genes as candidates to improve NUE. Further, the hitherto unavailable segregation of genetic and epigenetic gene targets could aid in informed interventions through genetic and epigenetic means of crop improvement.
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Affiliation(s)
- Narendra Sharma
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Bhumika Madan
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - M. Suhail Khan
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Kuljeet S. Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) - Mohali, Nagar, Punjab, India
| | - Nandula Raghuram
- Centre for Sustainable Nitrogen and Nutrient Management, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
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Flores-Díaz A, Escoto-Sandoval C, Cervantes-Hernández F, Ordaz-Ortiz JJ, Hayano-Kanashiro C, Reyes-Valdés H, Garcés-Claver A, Ochoa-Alejo N, Martínez O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1148. [PMID: 36904008 PMCID: PMC10005043 DOI: 10.3390/plants12051148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Gene co-expression networks are powerful tools to understand functional interactions between genes. However, large co-expression networks are difficult to interpret and do not guarantee that the relations found will be true for different genotypes. Statistically verified time expression profiles give information about significant changes in expressions through time, and genes with highly correlated time expression profiles, which are annotated in the same biological process, are likely to be functionally connected. A method to obtain robust networks of functionally related genes will be useful to understand the complexity of the transcriptome, leading to biologically relevant insights. We present an algorithm to construct gene functional networks for genes annotated in a given biological process or other aspects of interest. We assume that there are genome-wide time expression profiles for a set of representative genotypes of the species of interest. The method is based on the correlation of time expression profiles, bound by a set of thresholds that assure both, a given false discovery rate, and the discard of correlation outliers. The novelty of the method consists in that a gene expression relation must be repeatedly found in a given set of independent genotypes to be considered valid. This automatically discards relations particular to specific genotypes, assuring a network robustness, which can be set a priori. Additionally, we present an algorithm to find transcription factors candidates for regulating hub genes within a network. The algorithms are demonstrated with data from a large experiment studying gene expression during the development of the fruit in a diverse set of chili pepper genotypes. The algorithm is implemented and demonstrated in a new version of the publicly available R package "Salsa" (version 1.0).
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Affiliation(s)
- Alan Flores-Díaz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Christian Escoto-Sandoval
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Felipe Cervantes-Hernández
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - José J. Ordaz-Ortiz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Corina Hayano-Kanashiro
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo 83000, Mexico
| | - Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico
| | - Ana Garcés-Claver
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain
| | - Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
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Savoi S, Santiago A, Orduña L, Matus JT. Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits. FRONTIERS IN PLANT SCIENCE 2022; 13:937927. [PMID: 36340350 PMCID: PMC9630917 DOI: 10.3389/fpls.2022.937927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
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11
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Liu D, Cui Y, Zhao Z, Zhang J, Li S, Liu Z. Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet ( Setaria italica (L.) P. Beauv.). ROYAL SOCIETY OPEN SCIENCE 2022; 9:220953. [PMID: 36249327 PMCID: PMC9532984 DOI: 10.1098/rsos.220953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
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Affiliation(s)
- Dan Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin, People's Republic of China
| | - Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Zilong Zhao
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Jing Zhang
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
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Zhang Y, Han E, Peng Y, Wang Y, Wang Y, Geng Z, Xu Y, Geng H, Qian Y, Ma S. Rice co-expression network analysis identifies gene modules associated with agronomic traits. PLANT PHYSIOLOGY 2022; 190:1526-1542. [PMID: 35866684 PMCID: PMC9516743 DOI: 10.1093/plphys/kiac339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Identifying trait-associated genes is critical for rice (Oryza sativa) improvement, which usually relies on map-based cloning, quantitative trait locus analysis, or genome-wide association studies. Here we show that trait-associated genes tend to form modules within rice gene co-expression networks, a feature that can be exploited to discover additional trait-associated genes using reverse genetics. We constructed a rice gene co-expression network based on the graphical Gaussian model using 8,456 RNA-seq transcriptomes, which assembled into 1,286 gene co-expression modules functioning in diverse pathways. A number of the modules were enriched with genes associated with agronomic traits, such as grain size, grain number, tiller number, grain quality, leaf angle, stem strength, and anthocyanin content, and these modules are considered to be trait-associated gene modules. These trait-associated gene modules can be used to dissect the genetic basis of rice agronomic traits and to facilitate the identification of trait genes. As an example, we identified a candidate gene, OCTOPUS-LIKE 1 (OsOPL1), a homolog of the Arabidopsis (Arabidopsis thaliana) OCTOPUS gene, from a grain size module and verified it as a regulator of grain size via functional studies. Thus, our network represents a valuable resource for studying trait-associated genes in rice.
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Affiliation(s)
- Yu Zhang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Ershang Han
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yuming Peng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yuzhou Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yifan Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Zhenxing Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yupu Xu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Haiying Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
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13
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Singh KS, van der Hooft JJJ, van Wees SCM, Medema MH. Integrative omics approaches for biosynthetic pathway discovery in plants. Nat Prod Rep 2022; 39:1876-1896. [PMID: 35997060 PMCID: PMC9491492 DOI: 10.1039/d2np00032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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Xia W, Jiang H, Guo H, Liu Y, Gou X. Integrated gene co-expression network analysis reveals unique developmental processes of Aurelia aurita. Gene X 2022; 840:146733. [PMID: 35863715 DOI: 10.1016/j.gene.2022.146733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 06/15/2022] [Accepted: 07/08/2022] [Indexed: 11/04/2022] Open
Abstract
The typical life cycle of the moon jellyfish (Aurelia aurita) includes the planula, polyp, strobila, ephyra, and medusa developmental stages. These stages exhibit huge differences in both external morphology and internal physiological functions. However, the gene co-expression network involved in these post-embryonic developmental processes has not been studied yet. Here, based on 15 RNA sequencing samples covering all five stages of the A. aurita life cycle, we systematically analyzed the gene co-expression network and obtained 35 relevant modules. Furthermore, we identified the highly correlated modules and hub genes for each stage. These hub genes are implicated to play important roles in the developmental processes of A. aurita, which should help improve our understanding of the jellyfish life cycle.
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Affiliation(s)
- Wangxiao Xia
- Shaanxi Key Laboratory of Brain Disorders,Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an 710021, China
| | - Hui Jiang
- College of Life Science, Hainan Normal University, Haikou 571158, China
| | - Huifang Guo
- Shaanxi Key Laboratory of Infection and Immune Disorders, School of Basic Medical Science, Xi'an Medical University, Xi'an 710021, China
| | - Yaowen Liu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650231, China.
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders,Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an 710021, China.
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15
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Burks DJ, Sengupta S, De R, Mittler R, Azad RK. The Arabidopsis gene co-expression network. PLANT DIRECT 2022; 6:e396. [PMID: 35492683 PMCID: PMC9039629 DOI: 10.1002/pld3.396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Identifying genes that interact to confer a biological function to an organism is one of the main goals of functional genomics. High-throughput technologies for assessment and quantification of genome-wide gene expression patterns have enabled systems-level analyses to infer pathways or networks of genes involved in different functions under many different conditions. Here, we leveraged the publicly available, information-rich RNA-Seq datasets of the model plant Arabidopsis thaliana to construct a gene co-expression network, which was partitioned into clusters or modules that harbor genes correlated by expression. Gene ontology and pathway enrichment analyses were performed to assess functional terms and pathways that were enriched within the different gene modules. By interrogating the co-expression network for genes in different modules that associate with a gene of interest, diverse functional roles of the gene can be deciphered. By mapping genes differentially expressing under a certain condition in Arabidopsis onto the co-expression network, we demonstrate the ability of the network to uncover novel genes that are likely transcriptionally active but prone to be missed by standard statistical approaches due to their falling outside of the confidence zone of detection. To our knowledge, this is the first A. thaliana co-expression network constructed using the entire mRNA-Seq datasets (>20,000) available at the NCBI SRA database. The developed network can serve as a useful resource for the Arabidopsis research community to interrogate specific genes of interest within the network, retrieve the respective interactomes, decipher gene modules that are transcriptionally altered under certain condition or stage, and gain understanding of gene functions.
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Affiliation(s)
- David J. Burks
- Department of Biological Sciences and BioDiscovery Institute, College of ScienceUniversity of North TexasDentonTexasUSA
| | - Soham Sengupta
- Department of Biological Sciences and BioDiscovery Institute, College of ScienceUniversity of North TexasDentonTexasUSA
| | - Ronika De
- Department of Biological Sciences and BioDiscovery Institute, College of ScienceUniversity of North TexasDentonTexasUSA
| | - Ron Mittler
- The Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural ResourcesChristopher S. Bond Life Sciences Center University of MissouriColumbiaMissouriUSA
- Department of SurgeryUniversity of Missouri School of MedicineColumbiaMissouriUSA
| | - Rajeev K. Azad
- Department of Biological Sciences and BioDiscovery Institute, College of ScienceUniversity of North TexasDentonTexasUSA
- Department of MathematicsUniversity of North TexasDentonTexasUSA
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16
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Du Q, Campbell MT, Yu H, Liu K, Walia H, Zhang Q, Zhang C. Gene Co-expression Network Analysis and Linking Modules to Phenotyping Response in Plants. Methods Mol Biol 2022; 2539:261-268. [PMID: 35895209 DOI: 10.1007/978-1-0716-2537-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Environmental factors, including different stresses, can have an impact on the expression of genes and subsequently the phenotype and development of plants. Since a large number of genes are involved in response to the perturbation of the environment, identifying groups of co-expressed genes is meaningful. The gene co-expression network models can be used for the exploration, interpretation, and identification of genes responding to environmental changes. Once a gene co-expression network is constructed, one can determine gene modules and the association of gene modules to the phenotypic response. To link modules to phenotype, one approach is to find the correlated eigengenes of given modules or to integrate all eigengenes in regularized linear model. This manuscript describes the method from construction of co-expression network, module discovery, association between modules and phenotypic data, and finally to annotation/visualization.
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Affiliation(s)
- Qian Du
- School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE, USA
| | - Malachy T Campbell
- Department of Agronomy and Horticulture, Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE, USA
| | - Huihui Yu
- School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE, USA
| | - Kan Liu
- School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE, USA
| | - Qi Zhang
- Department of Mathematics and Statistics, College of Engineering and Physical Sciences (CEPS), University of New Hampshire, Durham, NH, USA
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, NE, USA.
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17
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Wang Y, Wang J, Hu H, Wang H, Wang C, Lin H, Zhao X. Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development. BMC Genom Data 2021; 22:32. [PMID: 34488628 PMCID: PMC8419915 DOI: 10.1186/s12863-021-00984-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 08/02/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Skeletal muscle growth and development are closely associated with the quantity and quality of pork production. We performed a transcriptomic analysis of 12 Longissimus dorsi muscle samples from Tibetan piglets at four postnatal stages of 0, 14, 30, and 60 days using RNA sequencing. RESULTS According to the pairwise comparisons between the libraries of the muscle samples at the four postnatal stages, a total of 4115 differentially expressed genes (DEGs) were identified in terms of |log2(fold change)| ≥ 1 and an adjusted P value < 0.01. Short-time series expression miner (STEM) analysis of the DEGs identified eight significantly different expression profiles, which were divided into two clusters based on the expression pattern. DEGs in cluster I displayed a pattern of decreasing to a nadir, and then a rise, and the significantly enriched gene ontology (GO) terms detected using them were involved in multiple processes, of which the cell cycle, immunocyte activation and proliferation, as well as actin cytoskeleton organization, were the top three overrepresented processes based on the GO terms functional classification. DEGs in cluster II displayed a pattern of increasing to a peak, then declining, which mainly contributed to protein metabolism. Furthermore, besides the pathways related to immune system, a few diseases, and protein metabolism, the DEGs in clusters I and II were significantly enriched in pathways related to muscle growth and development, such as the Rap1, PI3K-Akt, AMPK, and mTOR signaling pathways. CONCLUSIONS This study revealed GO terms and pathways that could affect the postnatal muscle growth and development in piglets. In addition, this study provides crucial information concerning the molecular mechanisms of muscle growth and development as well as an overview of the piglet transcriptome dynamics throughout the postnatal period in terms of growth and development.
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Affiliation(s)
- Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Hongmei Hu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Huaizhong Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Cheng Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Haichao Lin
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Xueyan Zhao
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China.
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18
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Lemoine GG, Scott-Boyer MP, Ambroise B, Périn O, Droit A. GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package. BMC Bioinformatics 2021; 22:267. [PMID: 34034647 PMCID: PMC8152313 DOI: 10.1186/s12859-021-04179-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/07/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Network-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between genes performing different biological functions. An extended description of each of the network modules is therefore a critical step to understand the underlying processes contributing to a disease or a phenotype. Biological integration, topology study and conditions comparison (e.g. wild vs mutant) are the main methods to do so, but to date no tool combines them all into a single pipeline. RESULTS Here we present GWENA, a new R package that integrates gene co-expression network construction and whole characterization of the detected modules through gene set enrichment, phenotypic association, hub genes detection, topological metric computation, and differential co-expression. To demonstrate its performance, we applied GWENA on two skeletal muscle datasets from young and old patients of GTEx study. Remarkably, we prioritized a gene whose involvement was unknown in the muscle development and growth. Moreover, new insights on the variations in patterns of co-expression were identified. The known phenomena of connectivity loss associated with aging was found coupled to a global reorganization of the relationships leading to expression of known aging related functions. CONCLUSION GWENA is an R package available through Bioconductor ( https://bioconductor.org/packages/release/bioc/html/GWENA.html ) that has been developed to perform extended analysis of gene co-expression networks. Thanks to biological and topological information as well as differential co-expression, the package helps to dissect the role of genes relationships in diseases conditions or targeted phenotypes. GWENA goes beyond existing packages that perform co-expression analysis by including new tools to fully characterize modules, such as differential co-expression, additional enrichment databases, and network visualization.
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Affiliation(s)
- Gwenaëlle G. Lemoine
- Département de médecine moléculaire, Faculté de médecine, Université Laval, 2325 rue de l’Université, Québec, G1V 0A6 Canada
| | - Marie-Pier Scott-Boyer
- Centre de recherche du Chu de Quebec-Université Laval, 2705 boulevard Laurier Québec, Québec, G1V 4G2 Canada
| | - Bathilde Ambroise
- L’Oréal Research and Innovation, 15 rue Pierre Dreyfus, 92110 Clichy, France
| | - Olivier Périn
- L’Oréal Research and Innovation, 15 rue Pierre Dreyfus, 92110 Clichy, France
| | - Arnaud Droit
- Département de médecine moléculaire, Faculté de médecine, Université Laval, 2325 rue de l’Université, Québec, G1V 0A6 Canada
- Centre de recherche du Chu de Quebec-Université Laval, 2705 boulevard Laurier Québec, Québec, G1V 4G2 Canada
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19
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Williams DR. Bayesian Estimation for Gaussian Graphical Models: Structure Learning, Predictability, and Network Comparisons. MULTIVARIATE BEHAVIORAL RESEARCH 2021; 56:336-352. [PMID: 33739907 DOI: 10.1080/00273171.2021.1894412] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gaussian graphical models (GGM; "networks") allow for estimating conditional dependence structures that are encoded by partial correlations. This is accomplished by identifying non-zero relations in the inverse of the covariance matrix. In psychology the default estimation method uses ℓ1-regularization, where the accompanying inferences are restricted to frequentist objectives. Bayesian methods remain relatively uncommon in practice and methodological literatures. To date, they have not yet been used for estimation and inference in the psychological network literature. In this work, I introduce Bayesian methodology that is specifically designed for the most common psychological applications. The graphical structure is determined with posterior probabilities that can be used to assess conditional dependent and independent relations. Additional methods are provided for extending inference to specific aspects within- and between-networks, including partial correlation differences and Bayesian methodology to quantify network predictability. I first demonstrate that the decision rule based on posterior probabilities can be calibrated to the desired level of specificity. The proposed techniques are then demonstrated in several illustrative examples. The methods have been implemented in the R package BGGM.
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Affiliation(s)
- Donald R Williams
- Department of Psychology, University of California, Davis, Davis, California, USA
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20
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Cortijo S, Bhattarai M, Locke JCW, Ahnert SE. Co-expression Networks From Gene Expression Variability Between Genetically Identical Seedlings Can Reveal Novel Regulatory Relationships. FRONTIERS IN PLANT SCIENCE 2020; 11:599464. [PMID: 33384705 PMCID: PMC7770228 DOI: 10.3389/fpls.2020.599464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Co-expression networks are a powerful tool to understand gene regulation. They have been used to identify new regulation and function of genes involved in plant development and their response to the environment. Up to now, co-expression networks have been inferred using transcriptomes generated on plants experiencing genetic or environmental perturbation, or from expression time series. We propose a new approach by showing that co-expression networks can be constructed in the absence of genetic and environmental perturbation, for plants at the same developmental stage. For this, we used transcriptomes that were generated from genetically identical individual plants that were grown under the same conditions and for the same amount of time. Twelve time points were used to cover the 24-h light/dark cycle. We used variability in gene expression between individual plants of the same time point to infer a co-expression network. We show that this network is biologically relevant and use it to suggest new gene functions and to identify new targets for the transcriptional regulators GI, PIF4, and PRR5. Moreover, we find different co-regulation in this network based on changes in expression between individual plants, compared to the usual approach requiring environmental perturbation. Our work shows that gene co-expression networks can be identified using variability in gene expression between individual plants, without the need for genetic or environmental perturbations. It will allow further exploration of gene regulation in contexts with subtle differences between plants, which could be closer to what individual plants in a population might face in the wild.
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Affiliation(s)
- Sandra Cortijo
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- UMR5004 Biochimie et Physiologie Moléculaire des Plantes, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Marcel Bhattarai
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - James C. W. Locke
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Sebastian E. Ahnert
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, University of Cambridge, Cambridge, United Kingdom
- The Alan Turing Institute, British Library, London, United Kingdom
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21
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Mondal R, Das P. Data-mining bioinformatics: suggesting Arabidopsis thaliana L-type lectin receptor kinase IX.2 ( LecRK-IX.2) modulate metabolites and abiotic stress responses. PLANT SIGNALING & BEHAVIOR 2020; 15:1818031. [PMID: 32924779 PMCID: PMC7671074 DOI: 10.1080/15592324.2020.1818031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 05/31/2023]
Abstract
The central role of the Arabidopsis LecRK-IX.2 gene in response to biotic stress has been well established by an array of workers. So far, the role of LecRK-IX.2 in abiotic stresses has not been investigated systematically. Here, we have first investigated a comprehensive in silico survey to explore the regulation, expression pattern in responses to a wide range of abiotic stresses. The present study reveals that the LecRK-IX.2 promoter has numerous potential cis-regulatory elements (CREs) that are regulated by different stresses. AtGenExpress data elucidate that LecRK-IX.2 gene plays a potential role in responses to cold, osmotic, drought, salt, UV-B, heat, wound, and genotoxic compound. The expression profile of the co-expressed genes suggests that Arabidopsis LecRK-IX.2 gene might have a potential role in stress responses in a tissue-specific manner. Furthermore, a probable signal transduction mechanism has been described by using protein-protein interaction (PPI) dataset. Moreover, the present data-mining investigations have suggested that LecRK-IX.2 gene modulates cellular metabolites and abiotic stress responses.
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Affiliation(s)
- Raju Mondal
- Mulberry Tissue Culture Lab, Mulberry Division, Central Sericultural Germplasm Resources Centre (CSGRC), Hosur, India
| | - Poushali Das
- Taxonomy and Biosystematic Laboratory, Department of Botany, University of Calcutta, Kolkata, India
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Zhang K, Qin X, Wen P, Wu Y, Zhuang J. Systematic analysis of molecular mechanisms of heart failure through the pathway and network-based approach. Life Sci 2020; 265:118830. [PMID: 33259868 DOI: 10.1016/j.lfs.2020.118830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022]
Abstract
AIMS The molecular networks and pathways involved in heart failure (HF) are still largely unknown. The present study aimed to systematically investigate the genes associated with HF, comprehensively explore their interactions and functions, and identify possible regulatory networks involved in HF. MAIN METHODS The weighted gene coexpression network analysis (WGCNA), crosstalk analysis, and Pivot analysis were used to identify gene connections, interaction networks, and molecular regulatory mechanisms. Functional analysis and protein-protein interaction (PPI) were performed using DAVID and STRING databases. Gene set variation analysis (GSVA) and receiver operating characteristic (ROC) curve analysis were also performed to evaluate the relationship of the hub genes with HF. KEY FINDINGS A total of 5968 HF-related genes were obtained to construct the co-expression networks, and 18 relatively independent and closely linked modules were identified. Pivot analysis suggested that four transcription factors and five noncoding RNAs were involved in regulating the process of HF. The genes in the module with the highest positive correlation to HF was mainly enriched in cardiac remodeling and response to stress. Five upregulated hub genes (ASPN, FMOD, NT5E, LUM, and OGN) were identified and validated. Furthermore, the GSVA scores of the five hub genes for HF had a relatively high areas under the curve (AUC). SIGNIFICANCE The results of this study revealed specific molecular networks and their potential regulatory mechanisms involved in HF. These may provide new insight into understanding the mechanisms underlying HF and help to identify more effective therapeutic targets for HF.
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Affiliation(s)
- Kai Zhang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xianyu Qin
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Pengju Wen
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yueheng Wu
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China.
| | - Jian Zhuang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China.
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Lee J, Shah M, Ballouz S, Crow M, Gillis J. CoCoCoNet: conserved and comparative co-expression across a diverse set of species. Nucleic Acids Res 2020; 48:W566-W571. [PMID: 32392296 PMCID: PMC7319556 DOI: 10.1093/nar/gkaa348] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data.
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Affiliation(s)
- John Lee
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
| | - Manthan Shah
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
| | - Sara Ballouz
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
| | - Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
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Lai X, Bendix C, Yan L, Zhang Y, Schnable JC, Harmon FG. Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs. BMC Genomics 2020; 21:428. [PMID: 32586356 PMCID: PMC7315539 DOI: 10.1186/s12864-020-06824-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/12/2020] [Indexed: 11/17/2022] Open
Abstract
Background The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum. Results Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran–Mantel–Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6–8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities. Conclusions This study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.
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Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Claire Bendix
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA
| | - Lang Yan
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Yang Zhang
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA
| | - James C Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.
| | - Frank G Harmon
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA. .,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA.
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Thakur V, Bains S, Pathania S, Sharma S, Kaur R, Singh K. Comparative transcriptomics reveals candidate transcription factors involved in costunolide biosynthesis in medicinal plant-Saussurea lappa. Int J Biol Macromol 2020; 150:52-67. [DOI: 10.1016/j.ijbiomac.2020.01.312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 01/01/2023]
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Bai L, Ren Y, Cui T. Overexpression of CDCA5, KIF4A, TPX2, and FOXM1 Coregulated Cell Cycle and Promoted Hepatocellular Carcinoma Development. J Comput Biol 2019; 27:965-974. [PMID: 31593490 DOI: 10.1089/cmb.2019.0254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
This study aimed to identify key functional modules and genes in functional module involved in hepatocellular carcinoma (HCC) development. The microarray data set GSE54236 was obtained from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between HCC, and normal samples were identified by Limma. DAVID was used to identify the gene ontology terms these genes enriched. The co-expression network was constructed based on Pearson correlation coefficient between gene expression values, and the functional modules these DEGs obviously enriched in were recognized through GraphWeb. Then, based on the genes related to the development of HCC, the DEGs interacting with HCC-associated genes were spotted. Finally, survival analysis and real-time quantitative polymerase chain reaction were performed. Totally, 427 upregulated (e.g., cell division cycle associated 5 [CDCA5], kinesin family member 4A [KIF4A], TPX2 microtubule nucleation factor [TPX2]) and 313 downregulated (e.g., metallothionein 1E [MT1E]) DEGs were identified in HCC. Besides, CDCA5, KIF4A, and TPX2 had interacting relationship and played important roles in HCC development by interrelating with HCC-related gene, forkhead box M1 (FOXM1). Furthermore, CDCA5, KIF4A, TPX2, and FOXM1 obviously enriched in cell cycle-related functional module, whereas MT1E enriched in mineral absorption module in Kyoto Encyclopedia of Genes and Genomes. CDCA5, KIF4A, and TPX2 expression were increased in HCC cells, and their high expressions were related to poor prognosis. Overexpression of CDCA5, KIF4A, TPX2, and FOXM1 coregulated cell cycle and thereby promoted the development of HCC. The finding provided potential targets for the study and treatment of HCC.
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Affiliation(s)
- Lianmei Bai
- Gastroenterology Department, Inner Mongolia People's Hospital, Hohhot, China
| | - Yu Ren
- Clinical Medical Research Center, Inner Mongolia People's Hospital, Hohhot, China
| | - Tianqing Cui
- Gastroenterology Department, Inner Mongolia People's Hospital, Hohhot, China
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Wu Z, Wang M, Yang S, Chen S, Chen X, Liu C, Wang S, Wang H, Zhang B, Liu H, Qin R, Wang X. A global coexpression network of soybean genes gives insights into the evolution of nodulation in nonlegumes and legumes. THE NEW PHYTOLOGIST 2019; 223:2104-2119. [PMID: 30977533 DOI: 10.1111/nph.15845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
A coexpression network is a powerful tool for revealing genes' relationship with many biological processes. Mass transcriptomic and genomic data from different plant species provide the foundation for understanding the evolution of nodulation across the Viridiplantae at a systematic level. We used weighted coexpression network analysis (WGCNA) to mine a nodule-related module (NRM) in Glycine max. Comparative genomic analysis of 78 green plant species revealed that NRM genes are recruited from different evolutionary nodes along with gene duplication events. A set of core coexpressed genes within legumes may play vital roles in regulating nodule environments essential for nitrogen fixation, including oxygen concentrations, sulfur transport, and iron homeostasis (such as GmCHY). The regulation of these genes occurred mainly at the transcription level, although some of them, such as sulfate transporters, may also undergo positive selection at protein level. We revealed that ancient orthologs and duplication events before the origin of legumes were preadapted for symbiosis. Conserved coregulated genes found within legumes paved the way for nodule formation and nitrogen fixation. These findings provide significant insights into the evolution of nodulation and indicate promising candidates for identifying other key components of legume nodulation and nitrogen fixation.
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Affiliation(s)
- Zhihua Wu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Meirong Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Siyu Yang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shengcai Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Xu Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Chang Liu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shixiang Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Haijiao Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Xuelu Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
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Yadav BS, Singh S, Srivastava S, Mani A. Analysis of chickpea gene co-expression networks and pathways during heavy metal stress. J Biosci 2019; 44:99. [PMID: 31502577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Crop productivity and yield are adversely affected by abiotic and biotic stresses. Therefore, finding out the genes responsible for stress tolerance is a significant stride towards crop improvement. A gene co-expression network is a powerful tool to detect the most connected genes during heavy metal (HM) stress in plants. The most connected genes may be responsible for HM tolerance by altering the different metabolic pathways during the biotic and abiotic stress. In the same line we have performed the GSE86807 microarray analysis of chickpea during exposure to chromium, cadmium and arsenic and analyzed the data. Common differentially expressed genes (DEGs) during exposure to chromium, cadmium and arsenic were identified and a co-expression network study was carried out. Hub and bottleneck genes were explored on the basis of degree and betweenness centrality, respectively. A gene set enrichment analysis study revealed that genes like haloacid dehydrogenase, cinnamoyl CoA reductase, F-box protein, GDSL esterase lipase, cellulose synthase, beta-glucosidase 13 and isoflavone hydroxylase are significantly enriched and regulate the different pathways like riboflavin metabolism, phenyl propanoid biosynthesis, amino acid biosynthesis, isoflavonoid biosynthesis and indole alkaloid biosynthesis.
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Affiliation(s)
- Birendra Singh Yadav
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad 211004, India
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Smita S, Katiyar A, Lenka SK, Dalal M, Kumar A, Mahtha SK, Yadav G, Chinnusamy V, Pandey DM, Bansal KC. Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis. Funct Integr Genomics 2019; 20:29-49. [PMID: 31286320 DOI: 10.1007/s10142-019-00697-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/31/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity of gene expression in tolerant and susceptible genotypes during meta-transcriptome analysis is important for understanding genotype-dependent stress tolerance mechanisms. Addressing this aspect, we describe here "abiotic stress tolerant" (ASTR) genes and networks specifically and differentially expressing in tolerant rice genotypes in response to different abiotic stress conditions. We identified 6,956 ASTR genes, key hub regulatory genes, transcription factors, and functional modules having significant association with abiotic stress-related ontologies and cis-motifs. Out of the 6956 ASTR genes, 73 were co-located within the boundary of previously identified abiotic stress trait-related quantitative trait loci. Functional annotation of 14 uncharacterized ASTR genes is proposed using multiple computational methods. Around 65% of the top ASTR genes were found to be differentially expressed in at least one of the tolerant genotypes under different stress conditions (cold, salt, drought, or heat) from publicly available RNAseq data comparison. The candidate ASTR genes specifically associated with tolerance could be utilized for engineering rice and possibly other crops for broad-spectrum tolerance to abiotic stresses.
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Affiliation(s)
- Shuchi Smita
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amit Katiyar
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- ICMR-AIIMS Computational Genomics Center, Div. of I.S.R.M., Indian Council of Medical Research, Ansari Nagar, New Delhi, 110029, India
| | - Sangram Keshari Lenka
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India
| | - Monika Dalal
- ICAR-National Research Center on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
| | - Amish Kumar
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjeet Kumar Mahtha
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Viswanathan Chinnusamy
- ICAR-Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Dev Mani Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kailash Chander Bansal
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India.
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India.
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Omony J, de Jong A, Kok J, van Hijum SAFT. Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network. PLoS One 2019; 14:e0214868. [PMID: 31116749 PMCID: PMC6530827 DOI: 10.1371/journal.pone.0214868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/21/2019] [Indexed: 01/30/2023] Open
Abstract
Lactic acid bacteria are Gram-positive bacteria used throughout the world in many industrial applications for their acidification, flavor and texture formation attributes. One of the species, Lactococcus lactis, is employed for the production of fermented milk products like cheese, buttermilk and quark. It ferments lactose to lactic acid and, thus, helps improve the shelf life of the products. Many physiological and transcriptome studies have been performed in L. lactis in order to comprehend and improve its biotechnological assets. Using large amounts of transcriptome data to understand and predict the behavior of biological processes in bacterial or other cell types is a complex task. Gene networks enable predicting gene behavior and function in the context of transcriptionally linked processes. We reconstruct and present the gene co-expression network (GCN) for the most widely studied L. lactis strain, MG1363, using publicly available transcriptome data. Several methods exist to generate and judge the quality of GCNs. Different reconstruction methods lead to networks with varying structural properties, consequently altering gene clusters. We compared the structural properties of the MG1363 GCNs generated by five methods, namely Pearson correlation, Spearman correlation, GeneNet, Weighted Gene Co-expression Network Analysis (WGCNA), and Sparse PArtial Correlation Estimation (SPACE). Using SPACE, we generated an L. lactis MG1363 GCN and assessed its quality using modularity and structural and biological criteria. The L. lactis MG1363 GCN has structural properties similar to those of the gold-standard networks of Escherichia coli K-12 and Bacillus subtilis 168. We showcase that the network can be used to mine for genes with similar expression profiles that are also generally linked to the same biological process.
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Affiliation(s)
- Jimmy Omony
- Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - Anne de Jong
- Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - Jan Kok
- Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
- * E-mail:
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Liu W, Lin L, Zhang Z, Liu S, Gao K, Lv Y, Tao H, He H. Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana. PLANTA 2019; 249:1487-1501. [PMID: 30701323 DOI: 10.1007/s00425-019-03102-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 01/28/2019] [Indexed: 05/22/2023]
Abstract
A comprehensive network of the Arabidopsis transcriptome was analyzed and may serve as a valuable resource for candidate gene function investigations. A web tool to explore module information was also provided. Arabidopsis thaliana is a widely studied model plant whose transcriptome has been substantially profiled in various tissues, development stages and other conditions. These data can be reused for research on gene function through a systematic analysis of gene co-expression relationships. We collected microarray data from National Center for Biotechnology Information Gene Expression Omnibus, identified modules of co-expressed genes and annotated module functions. These modules were associated with experiments/traits, which provided potential signature modules for phenotypes. Novel heat shock proteins were implicated according to guilt by association. A higher-order module networks analysis suggested that the Arabidopsis network can be further organized into 15 meta-modules and that a chloroplast meta-module has a distinct gene expression pattern from the other 14 meta-modules. A comparison with the rice transcriptome revealed preserved modules and KEGG pathways. All the module gene information was available from an online tool at http://bioinformatics.fafu.edu.cn/arabi/ . Our findings provide a new source for future gene discovery in Arabidopsis.
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Affiliation(s)
- Wei Liu
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
| | - Liping Lin
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Zhiyuan Zhang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Siqi Liu
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Kuan Gao
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Yanbin Lv
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Huan Tao
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Huaqin He
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
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Xia WX, Yu Q, Li GH, Liu YW, Xiao FH, Yang LQ, Rahman ZU, Wang HT, Kong QP. Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA. PeerJ 2019; 7:e6555. [PMID: 30886771 PMCID: PMC6421058 DOI: 10.7717/peerj.6555] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/02/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. METHODS Gene transcripts per million (TPM) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas, n = 77) and normal samples (Genotype Tissue Expression, n = 128). We used weighted gene co-expression network analysis to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein-protein interaction (PPI) network was constructed by the search tool for the retrieval of interacting genes. RESULTS To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes and nine modules. Among them, the blue module demonstrated significant correlation with the "Stage" of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.
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Affiliation(s)
- Wang-Xiao Xia
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Yao-Wen Liu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hao-Tian Wang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
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Shi M, Shen W, Chong Y, Wang HQ. Improving GRN re-construction by mining hidden regulatory signals. IET Syst Biol 2019; 11:174-181. [PMID: 29125126 PMCID: PMC8687237 DOI: 10.1049/iet-syb.2017.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Inferring gene regulatory networks (GRNs) from gene expression data is an important but challenging issue in systems biology. Here, the authors propose a dictionary learning-based approach that aims to infer GRNs by globally mining regulatory signals, known or latent. Gene expression is often regulated by various regulatory factors, some of which are observed and some of which are latent. The authors assume that all regulators are unknown for a target gene and the expression of the target gene can be mapped into a regulatory space spanned by all the regulators. Specifically, the authors modify the dictionary learning model, k-SVD, according to the sparse property of GRNs for mining the regulatory signals. The recovered regulatory signals are then used as a pool of regulatory factors to calculate a confidence score for a given transcription factor regulating a target gene. The capability of recovering hidden regulatory signals was verified on simulated data. Comparative experiments for GRN inference between the proposed algorithm (OURM) and some state-of-the-art algorithms, e.g. GENIE3 and ARACNE, on real-world data sets show the superior performance of OURM in inferring GRNs: higher area under the receiver operating characteristic curves and area under the precision-recall curves.
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Affiliation(s)
- Ming Shi
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, 129 Luoyu Road, Wuhan 430079, People's Republic of China
| | - Weiming Shen
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, 129 Luoyu Road, Wuhan 430079, People's Republic of China
| | - Yanwen Chong
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, 129 Luoyu Road, Wuhan 430079, People's Republic of China
| | - Hong-Qiang Wang
- Machine Intelligence and Computational Biology Laboratory, Institute of Intelligent Machines, Chinese Academy of Science, PO Box 1130, Hefei 230031, People's Republic of China.
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Gupta P, Singh SK. Gene Regulatory Networks: Current Updates and Applications in Plant Biology. ENERGY, ENVIRONMENT, AND SUSTAINABILITY 2019. [DOI: 10.1007/978-981-15-0690-1_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Mohanta TK, Bashir T, Hashem A, Abd Allah EF. Systems biology approach in plant abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 121:58-73. [PMID: 29096174 DOI: 10.1016/j.plaphy.2017.10.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/28/2017] [Accepted: 10/20/2017] [Indexed: 05/05/2023]
Abstract
Plant abiotic stresses are the major constraint on plant growth and development, causing enormous crop losses across the world. Plants have unique features to defend themselves against these challenging adverse stress conditions. They modulate their phenotypes upon changes in physiological, biochemical, molecular and genetic information, thus making them tolerant against abiotic stresses. It is of paramount importance to determine the stress-tolerant traits of a diverse range of genotypes of plant species and integrate those traits for crop improvement. Stress-tolerant traits can be identified by conducting genome-wide analysis of stress-tolerant genotypes through the highly advanced structural and functional genomics approach. Specifically, whole-genome sequencing, development of molecular markers, genome-wide association studies and comparative analysis of interaction networks between tolerant and susceptible crop varieties grown under stress conditions can greatly facilitate discovery of novel agronomic traits that protect plants against abiotic stresses.
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Affiliation(s)
- Tapan Kumar Mohanta
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Tufail Bashir
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Science, King Saud University, P.O. Box 24160, Riyadh, 11451, Saudi Arabia
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Silymarin-mediated regulation of the cell cycle and DNA damage response exerts antitumor activity in human hepatocellular carcinoma. Oncol Lett 2017; 15:885-892. [PMID: 29399153 PMCID: PMC5772825 DOI: 10.3892/ol.2017.7425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/26/2017] [Indexed: 02/02/2023] Open
Abstract
A novel module-search algorithm method was used to screen for potential signatures and investigate the molecular mechanisms of inhibiting hepatocellular carcinoma (HCC) growth following treatment with silymarin (SM). The modules algorithm was used to identify the modules via three major steps: i) Seed gene selection; ii) module search by seed expansion and entropy minimization; and iii) module refinement. The statistical significance of modules was computed to select the differential modules (DMs), followed by the identification of core modules using the attract method. Pathway analysis for core modules was implemented to identify the biological functions associated with the disease. Subsequently, results were verified in an independent sample set using reverse transcription polymerase chain reaction (RT-PCR). In total, 18 seed genes and 12 DMs (modules 1-12) were identified. The core modules were isolated using gene expression data. Overall, there were 4 core modules (modules 11, 5, 6 and 12). Additionally, DNA topoisomerase 2-binding protein 1 (TOPBP1), non-structural maintenance of chromosomes condensing I complex subunit H, nucleolar and spindle associated protein 1 (NUSAP1) and cell division cycle associated 3 (CDCA3) were the initial seed genes of module 11, 5, 6 and 12, respectively. Pathway results revealed that cell cycle signaling pathway was enriched by all core modules simultaneously. RT-PCR results indicated that the level of CDCA3, TOPBP1 and NUSAP1 in SM-treated HCC samples was markedly decreased compared with that in non-SM-treated HCC. No statistically significant difference between the transcriptional levels of CDCA3 in SM-treated and non-treated HCC groups was identified, although CDCA3 expression was increased in the treated group compared with the untreated group. Furthermore, although the expression level of TOPBP1 and NUSAP1 in the SM-treated group was decreased compared with that in the normal group, no significant difference was observed. From the results of the present study it can be inferred that TOPBP1, NUSAP1 and CDCA3 of the core modules may serve notable functions in SM-associated growth suppression of HCC.
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Ma S, Ding Z, Li P. Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. BMC PLANT BIOLOGY 2017; 17:131. [PMID: 28764653 PMCID: PMC5540570 DOI: 10.1186/s12870-017-1077-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a comprehensive analysis is lacking. RESULTS We constructed a maize gene co-expression network based on the graphical Gaussian model, using massive RNA-seq data. The network, containing 20,269 genes, assembles into 964 gene modules that function in a variety of plant processes, such as cell organization, the development of inflorescences, ligules and kernels, the uptake and utilization of nutrients (e.g. nitrogen and phosphate), the metabolism of benzoxazionids, oxylipins, flavonoids, and wax, and the response to stresses. Among them, the inflorescences development module is enriched with domestication genes (like ra1, ba1, gt1, tb1, tga1) that control plant architecture and kernel structure, while multiple other modules relate to diverse agronomic traits. Contained within these modules are transcription factors acting as known or potential expression regulators for the genes within the same modules, suggesting them as candidate regulators for related biological processes. A comparison with an established Arabidopsis network revealed conserved gene association patterns for specific modules involved in cell organization, nutrients uptake & utilization, and metabolism. The analysis also identified significant divergences between the two species for modules that orchestrate developmental pathways. CONCLUSIONS This network sheds light on how gene modules are organized between different species in the context of evolutionary divergence and highlights modules whose structure and gene content can provide important resources for maize gene functional studies with application potential.
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Affiliation(s)
- Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui China
| | - Zehong Ding
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong China
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Connectivity in gene coexpression networks negatively correlates with rates of molecular evolution in flowering plants. PLoS One 2017; 12:e0182289. [PMID: 28759647 PMCID: PMC5536297 DOI: 10.1371/journal.pone.0182289] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022] Open
Abstract
Gene coexpression networks are a useful tool for summarizing transcriptomic data and providing insight into patterns of gene regulation in a variety of species. Though there has been considerable interest in studying the evolution of network topology across species, less attention has been paid to the relationship between network position and patterns of molecular evolution. Here, we generated coexpression networks from publicly available expression data for seven flowering plant taxa (Arabidopsis thaliana, Glycine max, Oryza sativa, Populus spp., Solanum lycopersicum, Vitis spp., and Zea mays) to investigate the relationship between network position and rates of molecular evolution. We found a significant negative correlation between network connectivity and rates of molecular evolution, with more highly connected (i.e., “hub”) genes having significantly lower nonsynonymous substitution rates and dN/dS ratios compared to less highly connected (i.e., “peripheral”) genes across the taxa surveyed. These findings suggest that more centrally located hub genes are, on average, subject to higher levels of evolutionary constraint than are genes located on the periphery of gene coexpression networks. The consistency of this result across disparate taxa suggests that it holds for flowering plants in general, as opposed to being a species-specific phenomenon.
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Ahn H, Jung I, Shin SJ, Park J, Rhee S, Kim JK, Jung W, Kwon HB, Kim S. Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1044. [PMID: 28663756 PMCID: PMC5471331 DOI: 10.3389/fpls.2017.01044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/30/2017] [Indexed: 05/18/2023]
Abstract
This study was designed to investigate at the molecular level how a transgenic version of rice "Nipponbare" obtained a drought-resistant phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT) and a transgenic version (erf71) that had obtained a drought-resistant phenotype by overexpressing OsERF71, a member of the AP2/ERF transcription factor (TF) family. A comprehensive bioinformatics analysis pipeline, including TF networks and a cascade tree, was developed for the analysis of multi-omics data. The results of the analysis showed that the presence of OsERF71 at the source of the network controlled global gene expression levels in a specific manner to make erf71 survive longer than WT. Our analysis of the time-series transcriptome data suggests that erf71 diverted more energy to survival-critical mechanisms related to translation, oxidative response, and DNA replication, while further suppressing energy-consuming mechanisms, such as photosynthesis. To support this hypothesis further, we measured the net photosynthesis level under physiological conditions, which confirmed the further suppression of photosynthesis in erf71. In summary, our work presents a comprehensive snapshot of transcriptional modification in transgenic rice and shows how this induced the plants to acquire a drought-resistant phenotype.
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Affiliation(s)
- Hongryul Ahn
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Inuk Jung
- Interdisciplinary Program in Bioinformatics, Seoul National UniversitySeoul, South Korea
| | - Seon-Ju Shin
- Department of Biomedical Sciences, Sunmoon UniversityAsan, South Korea
| | - Jinwoo Park
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Sungmin Rhee
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National UniversitySeoul, South Korea
| | - Woosuk Jung
- Department of Applied Bioscience, Konkuk UniversitySeoul, South Korea
| | - Hawk-Bin Kwon
- Department of Biomedical Sciences, Sunmoon UniversityAsan, South Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National UniversitySeoul, South Korea
- Bioinformatics Institute, Seoul National UniversitySeoul, South Korea
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Narise T, Sakurai N, Obayashi T, Ohta H, Shibata D. Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene. BMC Genomics 2017; 18:437. [PMID: 28583129 PMCID: PMC5460524 DOI: 10.1186/s12864-017-3786-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/10/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Gene co-expression, the similarity of gene expression profiles under various experimental conditions, has been used as an indicator of functional relationships between genes, and many co-expression databases have been developed for predicting gene functions. These databases usually provide users with a co-expression network and a list of strongly co-expressed genes for a query gene. Several of these databases also provide functional information on a set of strongly co-expressed genes (i.e., provide biological processes and pathways that are enriched in these strongly co-expressed genes), which is generally analyzed via over-representation analysis (ORA). A limitation of this approach may be that users can predict gene functions only based on the strongly co-expressed genes. RESULTS In this study, we developed a new co-expression database that enables users to predict the function of tomato genes from the results of functional enrichment analyses of co-expressed genes while considering the genes that are not strongly co-expressed. To achieve this, we used the ORA approach with several thresholds to select co-expressed genes, and performed gene set enrichment analysis (GSEA) applied to a ranked list of genes ordered by the co-expression degree. We found that internal correlation in pathways affected the significance levels of the enrichment analyses. Therefore, we introduced a new measure for evaluating the relationship between the gene and pathway, termed the percentile (p)-score, which enables users to predict functionally relevant pathways without being affected by the internal correlation in pathways. In addition, we evaluated our approaches using receiver operating characteristic curves, which concluded that the p-score could improve the performance of the ORA. CONCLUSIONS We developed a new database, named Co-expressed Pathways DataBase for Tomato, which is available at http://cox-path-db.kazusa.or.jp/tomato . The database allows users to predict pathways that are relevant to a query gene, which would help to infer gene functions.
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Affiliation(s)
- Takafumi Narise
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Nozomu Sakurai
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Takeshi Obayashi
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
| | - Hiroyuki Ohta
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501 Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818 Japan
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Wisecaver JH, Borowsky AT, Tzin V, Jander G, Kliebenstein DJ, Rokas A. A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants. THE PLANT CELL 2017; 29:944-959. [PMID: 28408660 PMCID: PMC5466033 DOI: 10.1105/tpc.17.00009] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/12/2017] [Accepted: 04/09/2017] [Indexed: 05/20/2023]
Abstract
Plants produce diverse specialized metabolites (SMs), but the genes responsible for their production and regulation remain largely unknown, hindering efforts to tap plant pharmacopeia. Given that genes comprising SM pathways exhibit environmentally dependent coregulation, we hypothesized that genes within a SM pathway would form tight associations (modules) with each other in coexpression networks, facilitating their identification. To evaluate this hypothesis, we used 10 global coexpression data sets, each a meta-analysis of hundreds to thousands of experiments, across eight plant species to identify hundreds of coexpressed gene modules per data set. In support of our hypothesis, 15.3 to 52.6% of modules contained two or more known SM biosynthetic genes, and module genes were enriched in SM functions. Moreover, modules recovered many experimentally validated SM pathways, including all six known to form biosynthetic gene clusters (BGCs). In contrast, bioinformatically predicted BGCs (i.e., those lacking an associated metabolite) were no more coexpressed than the null distribution for neighboring genes. These results suggest that most predicted plant BGCs are not genuine SM pathways and argue that BGCs are not a hallmark of plant specialized metabolism. We submit that global gene coexpression is a rich, largely untapped resource for discovering the genetic basis and architecture of plant natural products.
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Affiliation(s)
- Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Alexander T Borowsky
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institute for Desert Research, Ben Gurion University, Sede-Boqer Campus 84990, Israel
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California-Davis, Davis, California 95616
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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Krishnan A, Gupta C, Ambavaram MMR, Pereira A. RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response. FRONTIERS IN PLANT SCIENCE 2017; 8:1640. [PMID: 28979289 PMCID: PMC5611544 DOI: 10.3389/fpls.2017.01640] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 09/06/2017] [Indexed: 05/22/2023]
Abstract
Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource - RECoN - that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 abiotic stress-specific gene modules covering 28,421 rice genes (>72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.
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Affiliation(s)
- Arjun Krishnan
- Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States
| | - Chirag Gupta
- Crop, Soil, and Environmental Sciences, University of Arkansas, FayettevilleAR, United States
| | | | - Andy Pereira
- Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States
- Crop, Soil, and Environmental Sciences, University of Arkansas, FayettevilleAR, United States
- *Correspondence: Andy Pereira,
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Abstract
A tremendous asset to the analysis of protein-protein interactions is the yeast-2-hybrid (Y2H) method. The Y2H assay is a heterologous system that is expanding network biology knowledge via in vivo investigations of binary protein-protein interactions. Traditionally, the Y2H protocol entails the mating or co-transformation of yeast in solid agar media followed by visual analysis for diploid selection. Having played a key role in identifying protein-protein interactions for nearly three decades in a wide range of biological systems, the Y2H system assays the interaction between two proteins of interest which results in a reconstituted and/or activation of transcription factor allowing a reporter gene to be transcribed. Overall, the Y2H method takes advantage of two factors: (1) the auxotrophic yeast requires expression of the reporter gene to grow in media purposefully designed to lack one or more essential amino acids, and (2) the DNA-binding (DB) domain of transcription factor GAL4 is unable to initiate transcription unless it is physically associated with an activating domain (AD), which, together, DBs and ADs are fused to proteins of interest that must interact with each other to reconstitute the transcription factor and activate the reporter gene. The applications of Y2H are broad, entailing fields such as drug discovery, clinical trials for human disease including cancer and neurodegenerative disease, and extend even into synthetic biology applications and cellular engineering. This chapter begins with an introduction to the fundamental mechanics of Y2H utilizing a genetically engineered strain of yeast and proceeds with an in-depth look at the different types of Y2H and turn our focus particularly to the GAL4-based Y2H system to map protein-protein interactions. We will then provide a step-by-step protocol for the Y2H experimentation preceded by a materials listing while simultaneously including key notes throughout the entire experimental process of biological-mechanistic and historical understandings of the steps.
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He F, Maslov S. Pan- and core- network analysis of co-expression genes in a model plant. Sci Rep 2016; 6:38956. [PMID: 27982071 PMCID: PMC5159811 DOI: 10.1038/srep38956] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/14/2016] [Indexed: 01/18/2023] Open
Abstract
Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of 'pan-network' and 'core-network' representing union and intersection between a sizeable fractions of individual networks, respectively. We showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.
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Affiliation(s)
- Fei He
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Sergei Maslov
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Bioengineering, Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Burks DJ, Azad RK. Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2016; 7:1857. [PMID: 28018393 PMCID: PMC5145899 DOI: 10.3389/fpls.2016.01857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/25/2016] [Indexed: 05/26/2023]
Abstract
The Auxin Response Factor (ARF) family of transcription factors is an important regulator of environmental response and symbiotic nodulation in the legume Medicago truncatula. While previous studies have identified members of this family, a recent spurt in gene expression data coupled with genome update and reannotation calls for a reassessment of the prevalence of ARF genes and their interaction networks in M. truncatula. We performed a comprehensive analysis of the M. truncatula genome and transcriptome that entailed search for novel ARF genes and the co-expression networks. Our investigation revealed 8 novel M. truncatula ARF (MtARF) genes, of the total 22 identified, and uncovered novel gene co-expression networks as well. Furthermore, the topological clustering and single enrichment analysis of several network models revealed the roles of individual members of the MtARF family in nitrogen regulation, nodule initiation, and post-embryonic development through a specialized protein packaging and secretory pathway. In summary, this study not just shines new light on an important gene family, but also provides a guideline for identification of new members of gene families and their functional characterization through network analyses.
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Affiliation(s)
- David J. Burks
- Department of Biological Sciences, University of North TexasDenton, TX, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North TexasDenton, TX, USA
- Department of Mathematics, University of North TexasDenton, TX, USA
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Uygun S, Peng C, Lehti-Shiu MD, Last RL, Shiu SH. Utility and Limitations of Using Gene Expression Data to Identify Functional Associations. PLoS Comput Biol 2016; 12:e1005244. [PMID: 27935950 PMCID: PMC5147789 DOI: 10.1371/journal.pcbi.1005244] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/13/2016] [Indexed: 01/25/2023] Open
Abstract
Gene co-expression has been widely used to hypothesize gene function through guilt-by association. However, it is not clear to what degree co-expression is informative, whether it can be applied to genes involved in different biological processes, and how the type of dataset impacts inferences about gene functions. Here our goal is to assess the utility and limitations of using co-expression as a criterion to recover functional associations between genes. By determining the percentage of gene pairs in a metabolic pathway with significant expression correlation, we found that many genes in the same pathway do not have similar transcript profiles and the choice of dataset, annotation quality, gene function, expression similarity measure, and clustering approach significantly impacts the ability to recover functional associations between genes using Arabidopsis thaliana as an example. Some datasets are more informative in capturing coordinated expression profiles and larger data sets are not always better. In addition, to recover the maximum number of known pathways and identify candidate genes with similar functions, it is important to explore rather exhaustively multiple dataset combinations, similarity measures, clustering algorithms and parameters. Finally, we validated the biological relevance of co-expression cluster memberships with an independent phenomics dataset and found that genes that consistently cluster with leucine degradation genes tend to have similar leucine levels in mutants. This study provides a framework for obtaining gene functional associations by maximizing the information that can be obtained from gene expression datasets. There remain genes with no known function even in the most well studied, model species. One common way to hypothesize gene function is based on the assumption that genes with similar expression profiles tend to have similar functions. However, using datasets and biological pathway information from the model plant Arabidopsis thaliana as an example, we discovered that, although genes in the same pathways are functionally related, genes in only a subset of the pathways have highly similar expression patterns. In addition, our ability to hypothesize gene functions based on expression is significantly impacted by how the dataset is processed and combined as well as the methodology used to identify genes with similar expression. Therefore, multiple datasets and methods should be tested to maximize the functional information that we can get based on similarity in gene expression.
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Affiliation(s)
- Sahra Uygun
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Cheng Peng
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Melissa D. Lehti-Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert L. Last
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Shin-Han Shiu
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Musungu BM, Bhatnagar D, Brown RL, Payne GA, OBrian G, Fakhoury AM, Geisler M. A Network Approach of Gene Co-expression in the Zea mays/ Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways. Front Genet 2016; 7:206. [PMID: 27917194 PMCID: PMC5116468 DOI: 10.3389/fgene.2016.00206] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/04/2016] [Indexed: 12/27/2022] Open
Abstract
A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays, and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of ROS. In addition to the ROS from Z. mays, there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus. Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire GEN for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus.
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Affiliation(s)
- Bryan M Musungu
- Department of Plant Biology, Southern Illinois University, CarbondaleIL, USA; Southern Regional Research Center, United States Department of Agriculture - Agricultural Research Service, New OrleansLA, USA
| | - Deepak Bhatnagar
- Southern Regional Research Center, United States Department of Agriculture - Agricultural Research Service, New Orleans LA, USA
| | - Robert L Brown
- Southern Regional Research Center, United States Department of Agriculture - Agricultural Research Service, New Orleans LA, USA
| | - Gary A Payne
- Department of Plant Pathology, North Carolina State University, Raleigh NC, USA
| | - Greg OBrian
- Department of Plant Pathology, North Carolina State University, Raleigh NC, USA
| | - Ahmad M Fakhoury
- Department of Plant Soil and Agriculture Systems, Southern Illinois University, Carbondale IL, USA
| | - Matt Geisler
- Department of Plant Biology, Southern Illinois University, Carbondale IL, USA
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Beiki H, Nejati-Javaremi A, Pakdel A, Masoudi-Nejad A, Hu ZL, Reecy JM. Large-scale gene co-expression network as a source of functional annotation for cattle genes. BMC Genomics 2016; 17:846. [PMID: 27806696 PMCID: PMC5094014 DOI: 10.1186/s12864-016-3176-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/18/2016] [Indexed: 11/15/2022] Open
Abstract
Background Genome sequencing and subsequent gene annotation of genomes has led to the elucidation of many genes, but in vertebrates the actual number of protein coding genes are very consistent across species (~20,000). Seven years after sequencing the cattle genome, there are still genes that have limited annotation and the function of many genes are still not understood, or partly understood at best. Based on the assumption that genes with similar patterns of expression across a vast array of tissues and experimental conditions are likely to encode proteins with related functions or participate within a given pathway, we constructed a genome-wide Cattle Gene Co-expression Network (CGCN) using 72 microarray datasets that contained a total of 1470 Affymetrix Genechip Bovine Genome Arrays that were retrieved from either NCBI GEO or EBI ArrayExpress. Results The total of 16,607 probe sets, which represented 11,397 genes, with unique Entrez ID were consolidated into 32 co-expression modules that contained between 29 and 2569 probe sets. All of the identified modules showed strong functional enrichment for gene ontology (GO) terms and Reactome pathways. For example, modules with important biological functions such as response to virus, response to bacteria, energy metabolism, cell signaling and cell cycle have been identified. Moreover, gene co-expression networks using “guilt-by-association” principle have been used to predict the potential function of 132 genes with no functional annotation. Four unknown Hub genes were identified in modules highly enriched for GO terms related to leukocyte activation (LOC509513), RNA processing (LOC100848208), nucleic acid metabolic process (LOC100850151) and organic-acid metabolic process (MGC137211). Such highly connected genes should be investigated more closely as they likely to have key regulatory roles. Conclusions We have demonstrated that the CGCN and its corresponding regulons provides rich information for experimental biologists to design experiments, interpret experimental results, and develop novel hypothesis on gene function in this poorly annotated genome. The network is publicly accessible at http://www.animalgenome.org/cgi-bin/host/reecylab/d. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3176-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hamid Beiki
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran.,Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Ardeshir Nejati-Javaremi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran.
| | - Abbas Pakdel
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, 31587-11167, Iran
| | - Zhi-Liang Hu
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
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