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Karatzas E, Baltoumas FA, Aplakidou E, Kontou PI, Stathopoulos P, Stefanis L, Bagos PG, Pavlopoulos GA. Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources. Bioinformatics 2023; 39:btad490. [PMID: 37540207 PMCID: PMC10423032 DOI: 10.1093/bioinformatics/btad490] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/31/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023] Open
Abstract
Functional enrichment is the process of identifying implicated functional terms from a given input list of genes or proteins. In this article, we present Flame (v2.0), a web tool which offers a combinatorial approach through merging and visualizing results from widely used functional enrichment applications while also allowing various flexible input options. In this version, Flame utilizes the aGOtool, g: Profiler, WebGestalt, and Enrichr pipelines and presents their outputs separately or in combination following a visual analytics approach. For intuitive representations and easier interpretation, it uses interactive plots such as parameterizable networks, heatmaps, barcharts, and scatter plots. Users can also: (i) handle multiple protein/gene lists and analyse union and intersection sets simultaneously through interactive UpSet plots, (ii) automatically extract genes and proteins from free text through text-mining and Named Entity Recognition (NER) techniques, (iii) upload single nucleotide polymorphisms (SNPs) and extract their relative genes, or (iv) analyse multiple lists of differentially expressed proteins/genes after selecting them interactively from a parameterizable volcano plot. Compared to the previous version of 197 supported organisms, Flame (v2.0) currently allows enrichment for 14 436 organisms. AVAILABILITY AND IMPLEMENTATION Web Application: http://flame.pavlopouloslab.info. Code: https://github.com/PavlopoulosLab/Flame. Docker: https://hub.docker.com/r/pavlopouloslab/flame.
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Affiliation(s)
- Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari (Athens), 16672, Greece
| | - Fotis A Baltoumas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari (Athens), 16672, Greece
| | - Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari (Athens), 16672, Greece
| | - Panagiota I Kontou
- Department of Mathematics, University of Thessaly, Lamia, 35100, Greece
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, 35131, Greece
| | - Panos Stathopoulos
- 1st Department of Neurology, Eginition Hospital, Athens, 11528, Greece
- School of Medicine, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - Leonidas Stefanis
- 1st Department of Neurology, Eginition Hospital, Athens, 11528, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, 35131, Greece
| | - Georgios A Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari (Athens), 16672, Greece
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
- Hellenic Army Academy, Vari, 16673, Greece
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Xiao H, Ma Y, Zhou Z, Li X, Ding K, Wu Y, Wu T, Chen D. Disease patterns of coronary heart disease and type 2 diabetes harbored distinct and shared genetic architecture. Cardiovasc Diabetol 2022; 21:276. [PMID: 36494812 PMCID: PMC9738029 DOI: 10.1186/s12933-022-01715-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Coronary heart disease (CHD) and type 2 diabetes (T2D) are two complex diseases with complex interrelationships. However, the genetic architecture of the two diseases is often studied independently by the individual single-nucleotide polymorphism (SNP) approach. Here, we presented a genotypic-phenotypic framework for deciphering the genetic architecture underlying the disease patterns of CHD and T2D. METHOD A data-driven SNP-set approach was performed in a genome-wide association study consisting of subpopulations with different disease patterns of CHD and T2D (comorbidity, CHD without T2D, T2D without CHD and all none). We applied nonsmooth nonnegative matrix factorization (nsNMF) clustering to generate SNP sets interacting the information of SNP and subject. Relationships between SNP sets and phenotype sets harboring different disease patterns were then assessed, and we further co-clustered the SNP sets into a genetic network to topologically elucidate the genetic architecture composed of SNP sets. RESULTS We identified 23 non-identical SNP sets with significant association with CHD or T2D (SNP-set based association test, P < 3.70 × [Formula: see text]). Among them, disease patterns involving CHD and T2D were related to distinct SNP sets (Hypergeometric test, P < 2.17 × [Formula: see text]). Accordingly, numerous genes (e.g., KLKs, GRM8, SHANK2) and pathways (e.g., fatty acid metabolism) were diversely implicated in different subtypes and related pathophysiological processes. Finally, we showed that the genetic architecture for disease patterns of CHD and T2D was composed of disjoint genetic networks (heterogeneity), with common genes contributing to it (pleiotropy). CONCLUSION The SNP-set approach deciphered the complexity of both genotype and phenotype as well as their complex relationships. Different disease patterns of CHD and T2D share distinct genetic architectures, for which lipid metabolism related to fibrosis may be an atherogenic pathway that is specifically activated by diabetes. Our findings provide new insights for exploring new biological pathways.
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Affiliation(s)
- Han Xiao
- grid.11135.370000 0001 2256 9319Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191 China
| | - Yujia Ma
- grid.11135.370000 0001 2256 9319Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191 China
| | - Zechen Zhou
- grid.11135.370000 0001 2256 9319Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191 China
| | - Xiaoyi Li
- grid.11135.370000 0001 2256 9319Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191 China
| | - Kexin Ding
- grid.11135.370000 0001 2256 9319Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191 China
| | - Yiqun Wu
- grid.11135.370000 0001 2256 9319Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191 China
| | - Tao Wu
- grid.11135.370000 0001 2256 9319Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191 China
| | - Dafang Chen
- grid.11135.370000 0001 2256 9319Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191 China
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Yang Y, Cai Y, Zhang Y, Yi X, Xu Z. Identification of Molecular Subtypes and Key Genes of Atherosclerosis Through Gene Expression Profiles. Front Mol Biosci 2021; 8:628546. [PMID: 33996893 PMCID: PMC8113832 DOI: 10.3389/fmolb.2021.628546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Atherosclerotic cardiovascular disease (ASCVD) caused by atherosclerosis (AS) is one of the highest causes of mortality worldwide. Although there have been many studies on AS, its etiology remains unclear. In order to carry out molecular characterization of different types of AS, we retrieved two datasets composed of 151 AS samples and 32 normal samples from the Gene Expression Omnibus database. Using the non-negative matrix factorization (NMF) algorithm, we successfully divided the 151 AS samples into two subgroups. We then compared the molecular characteristics between the two groups using weighted gene co-expression analysis (WGCNA) and identified six key modules associated with the two subgroups. Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analysis were used to identify the potential functions and pathways associated with the modules. In addition, we used the cytoscape software to construct and visualize protein-protein networks so as to identify key genes in the modules of interest. Three hub genes including PTGER3, GNAI1, and IGFBP5 were further screened using the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) algorithms. Since the modules were associated with immune pathways, we performed immune cell infiltration analysis. We discovered a significant difference in the level of immune cell infiltration by naïve B cells, CD8 T cells, T regulatory cells (Tregs), resting NK cells, Monocytes, Macrophages M0, Macrophages M1, and Macrophages M2 between the two subgroups. In addition, we observed the three hub genes were positively correlated with Tregs but negatively correlated with Macrophages M0. We also found that the three key genes are differentially expressed between normal and diseased tissue, as well as in the different subgroups. Receiver operating characteristic (ROC) results showed a good performance in the validation dataset. These results may provide novel insight into cellular and molecular characteristics of AS and potential markers for diagnosis and targeted therapy.
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Affiliation(s)
- Yujia Yang
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yue Cai
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuan Zhang
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xu Yi
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhiqiang Xu
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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Ray M, Sarkar S. Exploration of Differential Gene Expression with Functional Characterization and Pathways Enrichment from Microarray Profile of Papillary Thyroid Cancer: An In Silico Genomic Approach. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2019.100568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Pan Q, Wei J, Guo F, Huang S, Gong Y, Liu H, Liu J, Li L. Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. BMC Genomics 2019; 20:443. [PMID: 31159731 PMCID: PMC6547493 DOI: 10.1186/s12864-019-5812-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/20/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes. However, given the complexity of the molecular mechanisms underlying phenomes, only a few hundred gene-to-TO relationships in plants have been elucidated to date, limiting the pace of research in this "big data" era. RESULTS Here, we curated all the available trait associated sites (TAS) information from 79 association mapping studies of maize (Zea mays L.) and rice (Oryza sativa L.) lines with diverse genetic backgrounds and built a large-scale TAS-derived TO system for functional annotation of genes in various crops. Our TO system contains information for up to 18,042 genes (6345 in maize at the 25 k level and 11,697 in rice at the 50 k level), including gene-to-TO relationships, which covers over one fifth of the annotated gene sets for maize and rice. A comparison of Gene Ontology (GO) vs. TO analysis demonstrated that the TAS-derived TO system is an efficient alternative tool for gene functional annotation and enrichment analysis. We therefore combined information from the TO, GO, metabolic pathway, and co-expression network databases and constructed the TAS system, which is publicly available at http://tas.hzau.edu.cn . TAS provides a user-friendly interface for functional annotation of genes, enrichment analysis, genome-wide extraction of trait-associated genes, and crosschecking of different functional annotation databases. CONCLUSIONS TAS bridges the gap between genomic and phenomic information in crops. This easy-to-use tool will be useful for geneticists, biologists, and breeders in the agricultural community, as it facilitates the dissection of molecular mechanisms conferring agronomic traits in an easy, genome-wide manner.
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Affiliation(s)
- Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junfeng Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Suiyong Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Togayachi A, Tomioka A, Fujita M, Sukegawa M, Noro E, Takakura D, Miyazaki M, Shikanai T, Narimatsu H, Kaji H. Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1138-1152. [PMID: 29675740 PMCID: PMC6004004 DOI: 10.1007/s13361-018-1938-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 05/15/2023]
Abstract
To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE). This method used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures. To increase the number of identified peptide, fractionation of sample glycopeptides for reduction of sample complexity is required. Therefore, in this study, glycopeptides were fractionated into four fractions by hydrophilic interaction chromatography, and each fraction was analyzed using the Glyco-RIDGE method. As a result, many glycopeptides having long glycans were enriched in the highest hydrophilic fraction. Based on the monosaccharide composition, these glycans were thought to be poly-N-acetyllactosamine (polylactosamine [pLN]), and 31 pLN-carrier proteins were identified in HL-60 cells. Gene ontology enrichment analysis revealed that pLN carriers included many molecules related to signal transduction, receptors, and cell adhesion. Thus, these findings provided important insights into the analysis of the glycoproteome using our novel Glyco-RIDGE method. Graphical Abstract ᅟ.
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Affiliation(s)
- Akira Togayachi
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Azusa Tomioka
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Mika Fujita
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Masako Sukegawa
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Erika Noro
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Daisuke Takakura
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Michiyo Miyazaki
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Toshihide Shikanai
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hisashi Narimatsu
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
| | - Hiroyuki Kaji
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
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Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CYJ, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JI, Mariadason JM, Burgess AW, Mathivanan S. FunRich: An open access standalone functional enrichment and interaction network analysis tool. Proteomics 2015; 15:2597-601. [PMID: 25921073 DOI: 10.1002/pmic.201400515] [Citation(s) in RCA: 901] [Impact Index Per Article: 100.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/11/2015] [Accepted: 04/24/2015] [Indexed: 12/21/2022]
Abstract
As high-throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user-friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are integrated from heterogeneous genomic and proteomic resources (>1.5 million annotations). Besides default human specific FunRich database, users can download data from the UniProt database, which currently supports 20 different taxonomies against which enrichment analysis can be performed. Moreover, the users can build their own custom databases and perform the enrichment analysis irrespective of organism. In addition to proteomics datasets, the custom database allows for the tool to be used for genomics, lipidomics and metabolomics datasets. Thus, FunRich allows for complete database customization and thereby permits for the tool to be exploited as a skeleton for enrichment analysis irrespective of the data type or organism used. FunRich (http://www.funrich.org) is user-friendly and provides graphical representation (Venn, pie charts, bar graphs, column, heatmap and doughnuts) of the data with customizable font, scale and color (publication quality).
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Affiliation(s)
- Mohashin Pathan
- Department of Electronic Engineering, La Trobe University, Bundoora, Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Lahiru Gangoda
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Camelia Y J Quek
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - Nicholas A Williamson
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Dmitri Mouradov
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Oliver M Sieber
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Richard J Simpson
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Agus Salim
- Department of Mathematics and Statistics, La Trobe University, Bundoora, Australia
| | - Antony Bacic
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.,ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew F Hill
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, Monash University, Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash University, Australia
| | - Johnson I Agbinya
- Department of Electronic Engineering, La Trobe University, Bundoora, Australia
| | - John M Mariadason
- Olivia Newton John Cancer Research Institute, Melbourne, Australia, Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Australia, School of Cancer Medicine, La Trobe University, Melbourne, Australia
| | - Antony W Burgess
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Surgery (RMH), University of Melbourne, Parkville, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
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Kim HJ, Tang Y, Moon HS, Delhom CD, Fang DD. Functional analyses of cotton (Gossypium hirsutum L.) immature fiber (im) mutant infer that fiber cell wall development is associated with stress responses. BMC Genomics 2013; 14:889. [PMID: 24341782 PMCID: PMC3904472 DOI: 10.1186/1471-2164-14-889] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 12/07/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cotton fiber maturity is an important factor for determining the commercial value of cotton. How fiber cell wall development affects fiber maturity is not well understood. A comparison of fiber cross-sections showed that an immature fiber (im) mutant had lower fiber maturity than its near isogenic wild type, Texas marker-1 (TM-1). The availability of the im mutant and TM-1 provides a unique way to determine molecular mechanisms regulating cotton fiber maturity. RESULTS Transcriptome analysis showed that the differentially expressed genes (DEGs) in the im mutant fibers grown under normal stress conditions were similar to those in wild type cotton fibers grown under severe stress conditions. The majority of these DEGs in the im mutant were related to stress responses and cellular respiration. Stress is known to reduce the activity of a classical respiration pathway responsible for energy production and reactive oxygen species (ROS) accumulation. Both energy productions and ROS levels in the im mutant fibers are expected to be reduced if the im mutant is associated with stress responses. In accord with the prediction, the transcriptome profiles of the im mutant showed the same alteration of transcriptional regulation that happened in energy deprived plants in which expressions of genes associated with cell growth processes were reduced whereas expressions of genes associated with recycling and transporting processes were elevated. We confirmed that ROS production in developing fibers from the im mutant was lower than that from the wild type. The lower production of ROS in the im mutant fibers might result from the elevated levels of alternative respiration induced by stress. CONCLUSION The low degree of fiber cell wall thickness of the im mutant fibers is associated with deregulation of the genes involved in stress responses and cellular respiration. The reduction of ROS levels and up-regulation of the genes involved in alternative respirations suggest that energy deprivation may occur in the im mutant fibers.
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Affiliation(s)
- Hee Jin Kim
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, 1100 Robert E, Lee Blvd,, New Orleans, LA 70124, USA.
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Abstract
MOTIVATION The majority of next-generation sequencing technologies effectively sample small amounts of DNA or RNA that are amplified (i.e. copied) before sequencing. The amplification process is not perfect, leading to extreme bias in sequenced read counts. We present a novel procedure to account for amplification bias and demonstrate its effectiveness in mitigating gene length dependence when estimating true gene expression. RESULTS We tested the proposed method on simulated and real data. Simulations indicated that our method captures true gene expression more effectively than classic censoring-based approaches and leads to power gains in differential expression testing, particularly for shorter genes with high transcription rates. We applied our method to an unreplicated Arabidopsis RNA-seq dataset resulting in disparate gene ontologies arising from gene set enrichment analyses. AVAILABILITY AND IMPLEMENTATION R code to perform the RASTA procedures is freely available on the web at www.stat.purdue.edu/∼doerge/.
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Affiliation(s)
- Douglas D Baumann
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
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Naika M, Shameer K, Sowdhamini R. Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics. MOLECULAR BIOSYSTEMS 2013; 9:1888-908. [PMID: 23645342 DOI: 10.1039/c3mb70072k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biotic and abiotic stresses adversely affect agriculture by reducing crop growth and productivity worldwide. To investigate the abiotic stress-responsive genes in Arabidopsis thaliana, we compiled a dataset of stress signals and differentially upregulated genes (>= 2.5 fold change) from Stress-responsive transcription Factors DataBase (STIFDB) with additional set of stress signals and genes curated from PubMed and Gene Expression Omnibus. A dataset of 3091 genes differentially upregulated due to 14 different stress signals (abscisic acid, aluminum, cold, cold-drought-salt, dehydration, drought, heat, iron, light, NaCl, osmotic stress, oxidative stress, UV-B and wounding) were curated and used for the analysis. Details about stress-responsive enriched genes and their association with stress signals can be obtained from STIFDB2 database . The gene-stress-signal data were analyzed using an enrichment-based meta-analysis framework consisting of two different ontologies (Gene Ontology and Plant Ontology), biological pathway and functional domain annotations. We found several shared and distinct biological processes, cellular components and molecular functions associated with stress-responsive genes. Pathway analysis revealed that stress-responsive genes perturbed the pathways under the "Metabolic pathways" category. We also found several shared and stress-signal specific protein domains, suggesting functional mechanisms regulating stress-response. Phenomic characteristics of abiotic stress-responsive genes were ascertained for several stresses and found to be shared by multiple stresses in both anatomy and temporal categories of Plant Ontology. We found several constitutive stress-responsive genes that are differentially upregulated due to perturbation of different stress signals, for example a gene (AT1G68440) involved in phenylpropanoid metabolism and polyamine catabolism as responsive to seven different stress signals. We also performed structure-function prediction of five genes associated responsive to multiple abiotic stress signals. We envisage that results from our analysis that provide insight into functional repertoire, metabolic pathways and phenomic characteristics common and specifically associated with stress signals would help to understand abiotic stress regulome in Arabidopsis thaliana and may also help to develop an improved plant variety using molecular breeding and genetic engineering techniques that are rapidly stress-responsive and tolerant.
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Affiliation(s)
- Mahantesha Naika
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India.
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Ovezmyradov G, Lu Q, Göpfert MC. Mining Gene Ontology Data with AGENDA. Bioinform Biol Insights 2012; 6:63-7. [PMID: 22553422 PMCID: PMC3337784 DOI: 10.4137/bbi.s9101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The Gene Ontology (GO) initiative is a collaborative effort that uses controlled vocabularies for annotating genetic information. We here present AGENDA (Application for mining Gene Ontology Data), a novel web-based tool for accessing the GO database. AGENDA allows the user to simultaneously retrieve and compare gene lists linked to different GO terms in diverse species using batch queries, facilitating comparative approaches to genetic information. The web-based application offers diverse search options and allows the user to bookmark, visualize, and download the results. AGENDA is an open source web-based application that is freely available for non-commercial use at the project homepage. URL: http://sourceforge.net/projects/bioagenda.
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Affiliation(s)
- Guvanch Ovezmyradov
- Department of Cellular Neurobiology, Georg-August-University of Göttingen, Schwann-Schleiden Research Centre for Molecular Cell Biology, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
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Montero M, Coll A, Nadal A, Messeguer J, Pla M. Only half the transcriptomic differences between resistant genetically modified and conventional rice are associated with the transgene. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:693-702. [PMID: 21040388 DOI: 10.1111/j.1467-7652.2010.00572.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Besides the intended effects that give a genetically modified (GM) plant the desired trait, unintended differences between GM and non-GM comparable plants may also occur. Profiling technologies allow their identification, and a number of examples demonstrating that unintended effects are limited and diverse have recently been reported. Both from the food safety aspect and for research purposes, it is important to discern unintended changes produced by the transgene and its expression from those that may be attributed to other factors. Here, we show differential expression of around 0.40% transcriptome between conventional rice var. Senia and Senia-afp constitutively expressing the AFP antifungal protein. Analysis of one-fifth of the regulated sequences showed that around 35% of the unintended effects could be attributed to the process used to produce GM plants, based on in vitro tissue culture techniques. A further ∼15% were event specific, and their regulation was attributed to host gene disruption and genome rearrangements at the insertion site, and effects on proximal sequences. Thus, only around half the transcriptional unintended effects could be associated to the transgene itself. A significant number of changes in Senia-afp and Senia are part of the plant response to stress conditions, and around half the sequences for which up-regulation was attributed to the transgene were induced in conventional (but not transgenic) plants after wounding. Unintended effects might, as such, putatively result in widening the self-resistance characteristics because of the transgene in GM plants.
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Affiliation(s)
- Maria Montero
- Institut de Tecnologia Agroalimentària (INTEA), Universitat de Girona, Campus Montilivi, Girona, Spain
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Papatsenko I, Levine M, Papatsenko D. Temporal waves of coherent gene expression during Drosophila embryogenesis. Bioinformatics 2010; 26:2731-6. [PMID: 20819957 PMCID: PMC3025744 DOI: 10.1093/bioinformatics/btq513] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 08/30/2010] [Accepted: 08/31/2010] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Animal development depends on localized patterns of gene expression. Whole-genome methods permit the global identification of differential expression patterns. However, most gene-expression-clustering methods focus on the analysis of entire expression profiles, rather than temporal segments or time windows. RESULTS In the current study, local clustering of temporal time windows was applied to developing embryos of the fruitfly, Drosophila melanogaster. Large-scale developmental events, involving temporal activation of hundreds of genes, were identified as discrete gene clusters. The time-duration analysis revealed six temporal waves of coherent gene expression during Drosophila embryogenesis. The most powerful expression waves preceded major morphogenetic movements, such as germ band elongation and dorsal closure. These waves of gene expression coincide with the inhibition of maternal transcripts during early development, the specification of ectoderm, differentiation of the nervous system, differentiation of the digestive tract, deposition of the larval cuticle and the reorganization of the cytoskeleton during global morphogenetic events. We discuss the implications of these findings with respect to the gene regulatory networks governing Drosophila development. AVAILABILITY Data and software are available from the UC Berkeley web resource http://flydev.berkeley.edu/cgi-bin/GTEM/dmap_dm-ag/index_dmap.htm
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Affiliation(s)
- Ilya Papatsenko
- Department of Molecular and Cell Biology, University of California-Berkeley, CA, USA
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15
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Wren JD, Kupfer DM, Perkins EJ, Bridges S, Berleant D. Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 2010; 11 Suppl 6:S1. [PMID: 20946592 PMCID: PMC3026356 DOI: 10.1186/1471-2105-11-s6-s1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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16
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Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 2010; 38:W64-70. [PMID: 20435677 PMCID: PMC2896167 DOI: 10.1093/nar/gkq310] [Citation(s) in RCA: 1822] [Impact Index Per Article: 130.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data sets from high-throughput experiments. For agriGO, the system architecture and website interface were redesigned to improve performance and accessibility. The supported organisms and gene identifiers were substantially expanded (including 38 agricultural species composed of 274 data types). The requirement on user input is more flexible, in that user-defined reference and annotation are accepted. Moreover, a new analysis approach using Gene Set Enrichment Analysis strategy and customizable features is provided. Four tools, SEA (Singular enrichment analysis), PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA), are integrated as a toolkit to meet different demands. We also provide a cross-comparison service so that different data sets can be compared and explored in a visualized way. Lastly, agriGO functions as a GO data repository with search and download functions; agriGO is publicly accessible at http://bioinfo.cau.edu.cn/agriGO/.
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Affiliation(s)
- Zhou Du
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Wren JD, Gusev Y, Isokpehi RD, Berleant D, Braga-Neto U, Wilkins D, Bridges S. Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 2009; 10 Suppl 11:S1. [PMID: 19811674 PMCID: PMC3313274 DOI: 10.1186/1471-2105-10-s11-s1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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