151
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Riquelme Medina I, Lubovac-Pilav Z. Gene Co-Expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Type 1 Diabetes. PLoS One 2016; 11:e0156006. [PMID: 27257970 PMCID: PMC4892488 DOI: 10.1371/journal.pone.0156006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/06/2016] [Indexed: 12/16/2022] Open
Abstract
Type 1 diabetes (T1D) is a complex disease, caused by the autoimmune destruction of the insulin producing pancreatic beta cells, resulting in the body’s inability to produce insulin. While great efforts have been put into understanding the genetic and environmental factors that contribute to the etiology of the disease, the exact molecular mechanisms are still largely unknown. T1D is a heterogeneous disease, and previous research in this field is mainly focused on the analysis of single genes, or using traditional gene expression profiling, which generally does not reveal the functional context of a gene associated with a complex disorder. However, network-based analysis does take into account the interactions between the diabetes specific genes or proteins and contributes to new knowledge about disease modules, which in turn can be used for identification of potential new biomarkers for T1D. In this study, we analyzed public microarray data of T1D patients and healthy controls by applying a systems biology approach that combines network-based Weighted Gene Co-Expression Network Analysis (WGCNA) with functional enrichment analysis. Novel co-expression gene network modules associated with T1D were elucidated, which in turn provided a basis for the identification of potential pathways and biomarker genes that may be involved in development of T1D.
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Affiliation(s)
| | - Zelmina Lubovac-Pilav
- Bioinformatics research group, School of Biosciences, University of Skövde, Skövde, Sweden
- * E-mail:
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152
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Bhattacharyya M, Nath J, Bandyopadhyay S. Identifying significant microRNA–mRNA pairs associated with breast cancer subtypes. Mol Biol Rep 2016; 43:591-9. [DOI: 10.1007/s11033-016-4021-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 05/23/2016] [Indexed: 01/03/2023]
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153
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Ogris C, Helleday T, Sonnhammer ELL. PathwAX: a web server for network crosstalk based pathway annotation. Nucleic Acids Res 2016; 44:W105-9. [PMID: 27151197 PMCID: PMC4987909 DOI: 10.1093/nar/gkw356] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/19/2016] [Indexed: 12/22/2022] Open
Abstract
Pathway annotation of gene lists is often used to functionally analyse biomolecular data such as gene expression in order to establish which processes are activated in a given experiment. Databases such as KEGG or GO represent collections of how genes are known to be organized in pathways, and the challenge is to compare a given gene list with the known pathways such that all true relations are identified. Most tools apply statistical measures to the gene overlap between the gene list and pathway. It is however problematic to avoid false negatives and false positives when only using the gene overlap. The pathwAX web server (http://pathwAX.sbc.su.se/) applies a different approach which is based on network crosstalk. It uses the comprehensive network FunCoup to analyse network crosstalk between a query gene list and KEGG pathways. PathwAX runs the BinoX algorithm, which employs Monte-Carlo sampling of randomized networks and estimates a binomial distribution, for estimating the statistical significance of the crosstalk. This results in substantially higher accuracy than gene overlap methods. The system was optimized for speed and allows interactive web usage. We illustrate the usage and output of pathwAX.
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Affiliation(s)
- Christoph Ogris
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Thomas Helleday
- Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Erik L L Sonnhammer
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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154
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Mackinnon MJ, Ndila C, Uyoga S, Macharia A, Snow RW, Band G, Rautanen A, Rockett KA, Kwiatkowski DP, Williams TN. Environmental Correlation Analysis for Genes Associated with Protection against Malaria. Mol Biol Evol 2016; 33:1188-204. [PMID: 26744416 PMCID: PMC4839215 DOI: 10.1093/molbev/msw004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genome-wide searches for loci involved in human resistance to malaria are currently being conducted on a large scale in Africa using case-control studies. Here, we explore the utility of an alternative approach-"environmental correlation analysis, ECA," which tests for clines in allele frequencies across a gradient of an environmental selection pressure-to identify genes that have historically protected against death from malaria. We collected genotype data from 12,425 newborns on 57 candidate malaria resistance loci and 9,756 single nucleotide polymorphisms (SNPs) selected at random from across the genome, and examined their allele frequencies for geographic correlations with long-term malaria prevalence data based on 84,042 individuals living under different historical selection pressures from malaria in coastal Kenya. None of the 57 candidate SNPs showed significant (P < 0.05) correlations in allele frequency with local malaria transmission intensity after adjusting for population structure and multiple testing. In contrast, two of the random SNPs that had highly significant correlations (P < 0.01) were in genes previously linked to malaria resistance, namely, CDH13, encoding cadherin 13, and HS3ST3B1, encoding heparan sulfate 3-O-sulfotransferase 3B1. Both proteins play a role in glycoprotein-mediated cell-cell adhesion which has been widely implicated in cerebral malaria, the most life-threatening form of this disease. Other top genes, including CTNND2 which encodes δ-catenin, a molecular partner to cadherin, were significantly enriched in cadherin-mediated pathways affecting inflammation of the brain vascular endothelium. These results demonstrate the utility of ECA in the discovery of novel genes and pathways affecting infectious disease.
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Affiliation(s)
| | - Carolyne Ndila
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Sophie Uyoga
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Alex Macharia
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Robert W. Snow
- Department of Public Health Research, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Kirk A. Rockett
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominic P. Kwiatkowski
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Thomas N. Williams
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Medicine, Imperial College, London, United Kingdom
- INDEPTH Network, Kanda, Accra, Ghana
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155
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Al-Dalky R, Taha K, Al Homouz D, Qasaimeh M. Applying Monte Carlo Simulation to Biomedical Literature to Approximate Genetic Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:494-504. [PMID: 26415184 DOI: 10.1109/tcbb.2015.2481399] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Biologists often need to know the set of genes associated with a given set of genes or a given disease. We propose in this paper a classifier system called Monte Carlo for Genetic Network (MCforGN) that can construct genetic networks, identify functionally related genes, and predict gene-disease associations. MCforGN identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature. For a given gene g , the system first extracts the set of genes found within the abstracts of biomedical literature associated with g. It then ranks these genes to determine the ones with high co-occurrences with g . It overcomes the limitations of current approaches that employ analytical deterministic algorithms by applying Monte Carlo Simulation to approximate genetic networks. It does so by conducting repeated random sampling to obtain numerical results and to optimize these results. Moreover, it analyzes results to obtain the probabilities of different genes' co-occurrences using series of statistical tests. MCforGN can detect gene-disease associations by employing a combination of centrality measures (to identify the central genes in disease-specific genetic networks) and Monte Carlo Simulation. MCforGN aims at enhancing state-of-the-art biological text mining by applying novel extraction techniques. We evaluated MCforGN by comparing it experimentally with nine approaches. Results showed marked improvement.
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156
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Schweingruber C, Soffientini P, Ruepp MD, Bachi A, Mühlemann O. Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID). PLoS One 2016; 11:e0150239. [PMID: 26934103 PMCID: PMC4774922 DOI: 10.1371/journal.pone.0150239] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/02/2016] [Indexed: 01/09/2023] Open
Abstract
Proximity-dependent trans-biotinylation by the Escherichia coli biotin ligase BirA mutant R118G (BirA*) allows stringent streptavidin affinity purification of proximal proteins. This so-called BioID method provides an alternative to the widely used co-immunoprecipitation (co-IP) to identify protein-protein interactions. Here, we used BioID, on its own and combined with co-IP, to identify proteins involved in nonsense-mediated mRNA decay (NMD), a post-transcriptional mRNA turnover pathway that targets mRNAs that fail to terminate translation properly. In particular, we expressed BirA* fused to the well characterized NMD factors UPF1, UPF2 and SMG5 and detected by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) the streptavidin-purified biotinylated proteins. While the identified already known interactors confirmed the usefulness of BioID, we also found new potentially important interactors that have escaped previous detection by co-IP, presumably because they associate only weakly and/or very transiently with the NMD machinery. Our results suggest that SMG5 only transiently contacts the UPF1-UPF2-UPF3 complex and that it provides a physical link to the decapping complex. In addition, BioID revealed among others CRKL and EIF4A2 as putative novel transient interactors with NMD factors, but whether or not they have a function in NMD remains to be elucidated.
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Affiliation(s)
- Christoph Schweingruber
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Angela Bachi
- IFOM-FIRC Institute of Molecular Oncology, Milan, Italy
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- * E-mail:
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157
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De Maeyer D, Weytjens B, De Raedt L, Marchal K. Network-Based Analysis of eQTL Data to Prioritize Driver Mutations. Genome Biol Evol 2016; 8:481-94. [PMID: 26802430 PMCID: PMC4825419 DOI: 10.1093/gbe/evw010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive phenotype by affecting the same molecular pathways, a phenomenon referred to as parallelism at the molecular pathway level. This implies that successful driver identification depends on interpreting mutated genes in terms of molecular networks. Driver identification and obtaining a network-based understanding of the adaptive phenotype are thus confounded problems that ideally should be solved simultaneously. In this study, a network-based eQTL method is presented that solves both the driver identification and the network-based interpretation problem. As input the method uses coupled genotype-expression phenotype data (eQTL data) of independently evolved lines with similar adaptive phenotypes and an organism-specific genome-wide interaction network. The search for mutational consistency at pathway level is defined as a subnetwork inference problem, which consists of inferring a subnetwork from the genome-wide interaction network that best connects the genes containing mutations to differentially expressed genes. Based on their connectivity with the differentially expressed genes, mutated genes are prioritized as driver genes. Based on semisynthetic data and two publicly available data sets, we illustrate the potential of the network-based eQTL method to prioritize driver genes and to gain insights in the molecular mechanisms underlying an adaptive phenotype. The method is available at http://bioinformatics.intec.ugent.be/phenetic_eqtl/index.html
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Affiliation(s)
- Dries De Maeyer
- Deptartment of Information Technology (INTEC, iMINDS), UGent, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Weytjens
- Deptartment of Information Technology (INTEC, iMINDS), UGent, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Luc De Raedt
- Department of Computer Science, KU Leuven, Celestijnenlaan 200A, B-3001 Leuven, Belgium
| | - Kathleen Marchal
- Deptartment of Information Technology (INTEC, iMINDS), UGent, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium Department of Genetics, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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158
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Sui S, Wang X, Zheng H, Guo H, Chen T, Ji DM. Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia. Oncol Lett 2016; 10:3354-3362. [PMID: 26788135 PMCID: PMC4665311 DOI: 10.3892/ol.2015.3761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 07/16/2015] [Indexed: 01/23/2023] Open
Abstract
Pediatric acute lymphoblastic leukemia (ALL) accounts for over one-quarter of all pediatric cancers. Interacting genes and proteins within the larger human gene interaction network of the human genome are rarely investigated by studies investigating pediatric ALL. In the present study, interaction networks were constructed using the empirical Bayesian approach and the Search Tool for the Retrieval of Interacting Genes/proteins database, based on the differentially-expressed (DE) genes in pediatric ALL, which were identified using the RankProd package. Enrichment analysis of the interaction network was performed using the network-based methods EnrichNet and PathExpand, which were compared with the traditional expression analysis systematic explored (EASE) method. In total, 398 DE genes were identified in pediatric ALL, and LIF was the most significantly DE gene. The co-expression network consisted of 272 nodes, which indicated genes and proteins, and 602 edges, which indicated the number of interactions adjacent to the node. Comparison between EASE and PathExpand revealed that PathExpand detected more pathways or processes that were closely associated with pediatric ALL compared with the EASE method. There were 294 nodes and 1,588 edges in the protein-protein interaction network, with the processes of hematopoietic cell lineage and porphyrin metabolism demonstrating a close association with pediatric ALL. Network enrichment analysis based on the PathExpand algorithm was revealed to be more powerful for the analysis of interaction networks in pediatric ALL compared with the EASE method. LIF and MLLT11 were identified as the most significantly DE genes in pediatric ALL. The process of hematopoietic cell lineage was the pathway most significantly associated with pediatric ALL.
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Affiliation(s)
- Shuxiang Sui
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Xin Wang
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Hua Zheng
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Hua Guo
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Tong Chen
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Dong-Mei Ji
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
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159
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Stöckel D, Kehl T, Trampert P, Schneider L, Backes C, Ludwig N, Gerasch A, Kaufmann M, Gessler M, Graf N, Meese E, Keller A, Lenhof HP. Multi-omics enrichment analysis using the GeneTrail2 web service. Bioinformatics 2016; 32:1502-8. [PMID: 26787660 DOI: 10.1093/bioinformatics/btv770] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/28/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Gene set analysis has revolutionized the interpretation of high-throughput transcriptomic data. Nowadays, with comprehensive studies that measure multiple -omics from the same sample, powerful tools for the integrative analysis of multi-omics datasets are required. RESULTS Here, we present GeneTrail2, a web service allowing the integrated analysis of transcriptomic, miRNomic, genomic and proteomic datasets. It offers multiple statistical tests, a large number of predefined reference sets, as well as a comprehensive collection of biological categories and enables direct comparisons between the computed results. We used GeneTrail2 to explore pathogenic mechanisms of Wilms tumors. We not only succeeded in revealing signaling cascades that may contribute to the malignancy of blastemal subtype tumors but also identified potential biomarkers for nephroblastoma with adverse prognosis. The presented use-case demonstrates that GeneTrail2 is well equipped for the integrative analysis of comprehensive -omics data and may help to shed light on complex pathogenic mechanisms in cancer and other diseases. AVAILABILITY AND IMPLEMENTATION GeneTrail2 can be freely accessed under https://genetrail2.bioinf.uni-sb.de CONTACT : dstoeckel@bioinf.uni-sb.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Stöckel
- Center for Bioinformatics, Saarland University, Saarbrücken D-66041
| | - Tim Kehl
- Center for Bioinformatics, Saarland University, Saarbrücken D-66041
| | - Patrick Trampert
- Center for Bioinformatics, Saarland University, Saarbrücken D-66041
| | - Lara Schneider
- Center for Bioinformatics, Saarland University, Saarbrücken D-66041
| | - Christina Backes
- Center for Bioinformatics, Saarland University, Saarbrücken D-66041
| | - Nicole Ludwig
- Department of Human Genetics, Medical School, Saarland University, Homburg D-66421
| | - Andreas Gerasch
- Center for Bioinformatics, Eberhard-Karls-University, Tübingen, D-72076
| | - Michael Kaufmann
- Center for Bioinformatics, Eberhard-Karls-University, Tübingen, D-72076
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg D-97074 and
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Medical School, Saarland University, Homburg, D-66421, Germany
| | - Eckart Meese
- Department of Human Genetics, Medical School, Saarland University, Homburg D-66421
| | - Andreas Keller
- Center for Bioinformatics, Saarland University, Saarbrücken D-66041
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160
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Dong X, Hao Y, Wang X, Tian W. LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights. Sci Rep 2016; 6:18871. [PMID: 26750448 PMCID: PMC4707541 DOI: 10.1038/srep18871] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 11/27/2015] [Indexed: 12/27/2022] Open
Abstract
Pathway or gene set over-representation analysis (ORA) has become a routine task in functional genomics studies. However, currently widely used ORA tools employ statistical methods such as Fisher’s exact test that reduce a pathway into a list of genes, ignoring the constitutive functional non-equivalent roles of genes and the complex gene-gene interactions. Here, we develop a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets) that takes into consideration these two types of information by incorporating network-based gene weights in ORA analysis. In three benchmarks, LEGO achieves better performance than Fisher and three other network-based methods. To further evaluate LEGO’s usefulness, we compare LEGO with five gene expression-based and three pathway topology-based methods using a benchmark of 34 disease gene expression datasets compiled by a recent publication, and show that LEGO is among the top-ranked methods in terms of both sensitivity and prioritization for detecting target KEGG pathways. In addition, we develop a cluster-and-filter approach to reduce the redundancy among the enriched gene sets, making the results more interpretable to biologists. Finally, we apply LEGO to two lists of autism genes, and identify relevant gene sets to autism that could not be found by Fisher.
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Affiliation(s)
- Xinran Dong
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, P.R. China
| | - Yun Hao
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, P.R. China
| | - Xiao Wang
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, P.R. China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 100433, P.R. China.,Children's Hospital of Fudan University, Shanghai 200433, P.R. China
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161
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Hart T, Xie L. Providing data science support for systems pharmacology and its implications to drug discovery. Expert Opin Drug Discov 2016; 11:241-56. [PMID: 26689499 DOI: 10.1517/17460441.2016.1135126] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION The conventional one-drug-one-target-one-disease drug discovery process has been less successful in tracking multi-genic, multi-faceted complex diseases. Systems pharmacology has emerged as a new discipline to tackle the current challenges in drug discovery. The goal of systems pharmacology is to transform huge, heterogeneous, and dynamic biological and clinical data into interpretable and actionable mechanistic models for decision making in drug discovery and patient treatment. Thus, big data technology and data science will play an essential role in systems pharmacology. AREAS COVERED This paper critically reviews the impact of three fundamental concepts of data science on systems pharmacology: similarity inference, overfitting avoidance, and disentangling causality from correlation. The authors then discuss recent advances and future directions in applying the three concepts of data science to drug discovery, with a focus on proteome-wide context-specific quantitative drug target deconvolution and personalized adverse drug reaction prediction. EXPERT OPINION Data science will facilitate reducing the complexity of systems pharmacology modeling, detecting hidden correlations between complex data sets, and distinguishing causation from correlation. The power of data science can only be fully realized when integrated with mechanism-based multi-scale modeling that explicitly takes into account the hierarchical organization of biological systems from nucleic acid to proteins, to molecular interaction networks, to cells, to tissues, to patients, and to populations.
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Affiliation(s)
- Thomas Hart
- a The Rockefeller University , New York , NY , USA.,b Department of Biological Sciences, Hunter College , The City University of New York , New York , NY , USA
| | - Lei Xie
- c Department of Computer Science, Hunter College , The City University of New York , New York , NY , USA.,d The Graduate Center , The City University of New York , New York , NY , USA
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162
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Yue Z, Kshirsagar MM, Nguyen T, Suphavilai C, Neylon MT, Zhu L, Ratliff T, Chen JY. PAGER: constructing PAGs and new PAG-PAG relationships for network biology. Bioinformatics 2015; 31:i250-7. [PMID: 26072489 PMCID: PMC4553834 DOI: 10.1093/bioinformatics/btv265] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In this article, we described a new database framework to perform integrative “gene-set, network, and pathway analysis” (GNPA). In this framework, we integrated heterogeneous data on pathways, annotated list, and gene-sets (PAGs) into a PAG electronic repository (PAGER). PAGs in the PAGER database are organized into P-type, A-type and G-type PAGs with a three-letter-code standard naming convention. The PAGER database currently compiles 44 313 genes from 5 species including human, 38 663 PAGs, 324 830 gene–gene relationships and two types of 3 174 323 PAG–PAG regulatory relationships—co-membership based and regulatory relationship based. To help users assess each PAG’s biological relevance, we developed a cohesion measure called Cohesion Coefficient (CoCo), which is capable of disambiguating between biologically significant PAGs and random PAGs with an area-under-curve performance of 0.98. PAGER database was set up to help users to search and retrieve PAGs from its online web interface. PAGER enable advanced users to build PAG–PAG regulatory networks that provide complementary biological insights not found in gene set analysis or individual gene network analysis. We provide a case study using cancer functional genomics data sets to demonstrate how integrative GNPA help improve network biology data coverage and therefore biological interpretability. The PAGER database can be accessible openly at http://discovery.informatics.iupui.edu/PAGER/. Contact: jakechen@iupui.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zongliang Yue
- Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China
| | - Madhura M Kshirsagar
- Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China
| | - Thanh Nguyen
- Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China
| | - Chayaporn Suphavilai
- Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China
| | - Michael T Neylon
- Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China
| | - Liugen Zhu
- Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China
| | - Timothy Ratliff
- Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China
| | - Jake Y Chen
- Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China
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163
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Al-Harazi O, Al Insaif S, Al-Ajlan MA, Kaya N, Dzimiri N, Colak D. Integrated Genomic and Network-Based Analyses of Complex Diseases and Human Disease Network. J Genet Genomics 2015; 43:349-67. [PMID: 27318646 DOI: 10.1016/j.jgg.2015.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 10/22/2015] [Accepted: 11/20/2015] [Indexed: 12/16/2022]
Abstract
A disease phenotype generally reflects various pathobiological processes that interact in a complex network. The highly interconnected nature of the human protein interaction network (interactome) indicates that, at the molecular level, it is difficult to consider diseases as being independent of one another. Recently, genome-wide molecular measurements, data mining and bioinformatics approaches have provided the means to explore human diseases from a molecular basis. The exploration of diseases and a system of disease relationships based on the integration of genome-wide molecular data with the human interactome could offer a powerful perspective for understanding the molecular architecture of diseases. Recently, subnetwork markers have proven to be more robust and reliable than individual biomarker genes selected based on gene expression profiles alone, and achieve higher accuracy in disease classification. We have applied one of these methodologies to idiopathic dilated cardiomyopathy (IDCM) data that we have generated using a microarray and identified significant subnetworks associated with the disease. In this paper, we review the recent endeavours in this direction, and summarize the existing methodologies and computational tools for network-based analysis of complex diseases and molecular relationships among apparently different disorders and human disease network. We also discuss the future research trends and topics of this promising field.
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Affiliation(s)
- Olfat Al-Harazi
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sadiq Al Insaif
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Monirah A Al-Ajlan
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; College of Computer and Information Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nduna Dzimiri
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia.
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164
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Chaudhuri R, Khoo PS, Tonks K, Junutula JR, Kolumam G, Modrusan Z, Samocha-Bonet D, Meoli CC, Hocking S, Fazakerley DJ, Stöckli J, Hoehn KL, Greenfield JR, Yang JYH, James DE. Cross-species gene expression analysis identifies a novel set of genes implicated in human insulin sensitivity. NPJ Syst Biol Appl 2015; 1:15010. [PMID: 28725461 PMCID: PMC5516867 DOI: 10.1038/npjsba.2015.10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 07/24/2015] [Accepted: 08/24/2015] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Insulin resistance (IR) is one of the earliest predictors of type 2 diabetes. However, diagnosis of IR is limited. High fat fed mouse models provide key insights into IR. We hypothesized that early features of IR are associated with persistent changes in gene expression (GE) and endeavored to (a) develop novel methods for improving signal:noise in analysis of human GE using mouse models; (b) identify a GE motif that accurately diagnoses IR in humans; and (c) identify novel biology associated with IR in humans. METHODS We integrated human muscle GE data with longitudinal mouse GE data and developed an unbiased three-level cross-species analysis platform (single gene, gene set, and networks) to generate a gene expression motif (GEM) indicative of IR. A logistic regression classification model validated GEM in three independent human data sets (n=115). RESULTS This GEM of 93 genes substantially improved diagnosis of IR compared with routine clinical measures across multiple independent data sets. Individuals misclassified by GEM possessed other metabolic features raising the possibility that they represent a separate metabolic subclass. The GEM was enriched in pathways previously implicated in insulin action and revealed novel associations between β-catenin and Jak1 and IR. Functional analyses using small molecule inhibitors showed an important role for these proteins in insulin action. CONCLUSIONS This study shows that systems approaches for identifying molecular signatures provides a powerful way to stratify individuals into discrete metabolic groups. Moreover, we speculate that the β-catenin pathway may represent a novel biomarker for IR in humans that warrant future investigation.
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Affiliation(s)
- Rima Chaudhuri
- Charles Perkins Centre, School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia.,Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Poh Sim Khoo
- Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Katherine Tonks
- Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Department of Endocrinology and Diabetes Centre, St Vincent's Hospital, Sydney, NSW, Australia
| | | | | | - Zora Modrusan
- Genentech Incorporated, South San Francisco, CA, USA
| | - Dorit Samocha-Bonet
- Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Christopher C Meoli
- Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Samantha Hocking
- Department of Endocrinology, Royal North Shore Hospital, Sydney, NSW, Australia.,School of Medicine, The University of Sydney, Sydney, NSW, Australia
| | - Daniel J Fazakerley
- Charles Perkins Centre, School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia.,Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Jacqueline Stöckli
- Charles Perkins Centre, School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia.,Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Kyle L Hoehn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jerry R Greenfield
- Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Department of Endocrinology and Diabetes Centre, St Vincent's Hospital, Sydney, NSW, Australia.,Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
| | - David E James
- Charles Perkins Centre, School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia.,Diabetes and Obesity Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Medicine, The University of Sydney, Sydney, NSW, Australia
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165
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Yu X, Zeng T, Li G. Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples. BMC Genomics 2015; 16:918. [PMID: 26556243 PMCID: PMC4641376 DOI: 10.1186/s12864-015-2188-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 11/02/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Pathway enrichment analysis is a useful tool to study biology and biomedicine, due to its functional screening on well-defined biological procedures rather than separate molecules. The measurement of malfunctions of pathways with a phenotype change, e.g., from normal to diseased, is the key issue when applying enrichment analysis on a pathway. The differentially expressed genes (DEGs) are widely focused in conventional analysis, which is based on the great purity of samples. However, the disease samples are usually heterogeneous, so that, the genes with great differential expression variance (DEVGs) are becoming attractive and important to indicate the specific state of a biological system. In the context of differential expression variance, it is still a challenge to measure the enrichment or status of a pathway. To address this issue, we proposed Integrative Enrichment Analysis (IEA) based on a novel enrichment measurement. RESULTS The main competitive ability of IEA is to identify dysregulated pathways containing DEGs and DEVGs simultaneously, which are usually under-scored by other methods. Next, IEA provides two additional assistant approaches to investigate such dysregulated pathways. One is to infer the association among identified dysregulated pathways and expected target pathways by estimating pathway crosstalks. The other one is to recognize subtype-factors as dysregulated pathways associated to particular clinical indices according to the DEVGs' relative expressions rather than conventional raw expressions. Based on a previously established evaluation scheme, we found that, in particular cohorts (i.e., a group of real gene expression datasets from human patients), a few target disease pathways can be significantly high-ranked by IEA, which is more effective than other state-of-the-art methods. Furthermore, we present a proof-of-concept study on Diabetes to indicate: IEA rather than conventional ORA or GSEA can capture the under-estimated dysregulated pathways full of DEVGs and DEGs; these newly identified pathways could be significantly linked to prior-known disease pathways by estimated crosstalks; and many candidate subtype-factors recognized by IEA also have significant relation with the risk of subtypes of genotype-phenotype associations. CONCLUSIONS Totally, IEA supplies a new tool to carry on enrichment analysis in the complicate context of clinical application (i.e., heterogeneity of disease), as a necessary complementary and cooperative approach to conventional ones.
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Affiliation(s)
- Xiangtian Yu
- School of Mathematics, Shandong University, Jinan, 250100, China.
| | - Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Cell Building Level 3, YueYang Road 320, Shanghai, 200031, China.
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100, China.
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166
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Mooney MA, Wilmot B. Gene set analysis: A step-by-step guide. Am J Med Genet B Neuropsychiatr Genet 2015; 168:517-27. [PMID: 26059482 PMCID: PMC4638147 DOI: 10.1002/ajmg.b.32328] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/20/2015] [Indexed: 12/21/2022]
Abstract
To maximize the potential of genome-wide association studies, many researchers are performing secondary analyses to identify sets of genes jointly associated with the trait of interest. Although methods for gene-set analyses (GSA), also called pathway analyses, have been around for more than a decade, the field is still evolving. There are numerous algorithms available for testing the cumulative effect of multiple SNPs, yet no real consensus in the field about the best way to perform a GSA. This paper provides an overview of the factors that can affect the results of a GSA, the lessons learned from past studies, and suggestions for how to make analysis choices that are most appropriate for different types of data. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Michael A. Mooney
- Department of Medical Informatics & Clinical Epidemiology, Division of Bioinformatics & Computational Biology, Oregon Health & Science University, Portland, Oregon,OHSU Knight Cancer Institute, Portland, Oregon
| | - Beth Wilmot
- Department of Medical Informatics & Clinical Epidemiology, Division of Bioinformatics & Computational Biology, Oregon Health & Science University, Portland, Oregon,OHSU Knight Cancer Institute, Portland, Oregon,Oregon Clinical and Translational Research Institute, Portland, Oregon,Correspondence to: Beth Wilmot, Department of Medical Informatics & Clinical Epidemiology, Division of Bioinformatics & Computational Biology, Oregon Health & Science University, Portland, OR 97239.
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167
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Suleiman SH, Koko ME, Nasir WH, Elfateh O, Elgizouli UK, Abdallah MOE, Alfarouk KO, Hussain A, Faisal S, Ibrahim FMA, Romano M, Sultan A, Banks L, Newport M, Baralle F, Elhassan AM, Mohamed HS, Ibrahim ME. Exome sequencing of a colorectal cancer family reveals shared mutation pattern and predisposition circuitry along tumor pathways. Front Genet 2015; 6:288. [PMID: 26442106 PMCID: PMC4584935 DOI: 10.3389/fgene.2015.00288] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/28/2015] [Indexed: 01/04/2023] Open
Abstract
The molecular basis of cancer and cancer multiple phenotypes are not yet fully understood. Next Generation Sequencing promises new insight into the role of genetic interactions in shaping the complexity of cancer. Aiming to outline the differences in mutation patterns between familial colorectal cancer cases and controls we analyzed whole exomes of cancer tissues and control samples from an extended colorectal cancer pedigree, providing one of the first data sets of exome sequencing of cancer in an African population against a background of large effective size typically with excess of variants. Tumors showed hMSH2 loss of function SNV consistent with Lynch syndrome. Sets of genes harboring insertions-deletions in tumor tissues revealed, however, significant GO enrichment, a feature that was not seen in control samples, suggesting that ordered insertions-deletions are central to tumorigenesis in this type of cancer. Network analysis identified multiple hub genes of centrality. ELAVL1/HuR showed remarkable centrality, interacting specially with genes harboring non-synonymous SNVs thus reinforcing the proposition of targeted mutagenesis in cancer pathways. A likely explanation to such mutation pattern is DNA/RNA editing, suggested here by nucleotide transition-to-transversion ratio that significantly departed from expected values (p-value 5e-6). NFKB1 also showed significant centrality along with ELAVL1, raising the suspicion of viral etiology given the known interaction between oncogenic viruses and these proteins.
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Affiliation(s)
| | - Mahmoud E Koko
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Wafaa H Nasir
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Ommnyiah Elfateh
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Ubai K Elgizouli
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Mohammed O E Abdallah
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Khalid O Alfarouk
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Ayman Hussain
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Shima Faisal
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Fathelrahamn M A Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum Khartoum, Sudan
| | - Maurizio Romano
- International Centre for Genetic Engineering and Biotechnology Trieste, Italy
| | - Ali Sultan
- Weill Cornell Medical College Doha, Qatar
| | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology Trieste, Italy
| | | | - Francesco Baralle
- International Centre for Genetic Engineering and Biotechnology Trieste, Italy
| | | | - Hiba S Mohamed
- Faculty of Medicine, University of Khartoum Khartoum, Sudan
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168
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Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD. Pathway and network analysis of cancer genomes. Nat Methods 2015; 12:615-621. [PMID: 26125594 DOI: 10.1038/nmeth.3440] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.
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Affiliation(s)
- Pau Creixell
- Cellular Signal Integration Group (C-SIG), Technical University of Denmark, Lyngby, Denmark
| | - Jüri Reimand
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Syed Haider
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Guanming Wu
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center, Chuo-ku, Tokyo, Japan
| | - Miguel Vazquez
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Ville Mustonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Abel Gonzalez-Perez
- Research Unit on Biomedical Informatics, University Pompeu Fabra, Barcelona, Spain
| | - John Pearson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Benjamin J Raphael
- Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA USA
| | - B F Francis Ouellette
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Joshua M Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.,Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA
| | - Rune Linding
- Cellular Signal Integration Group (C-SIG), Technical University of Denmark, Lyngby, Denmark.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), DK-2200 Copenhagen, Denmark
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, University Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Lincoln D Stein
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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169
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Guo L, Song C, Wang P, Dai L, Zhang J, Wang K. A systems biology approach to detect key pathways and interaction networks in gastric cancer on the basis of microarray analysis. Mol Med Rep 2015; 12:7139-45. [PMID: 26324226 DOI: 10.3892/mmr.2015.4242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 07/31/2015] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to explore key molecular pathways contributing to gastric cancer (GC) and to construct an interaction network between significant pathways and potential biomarkers. Publicly available gene expression profiles of GSE29272 for GC, and data for the corresponding normal tissue, were downloaded from Gene Expression Omnibus. Pre‑processing and differential analysis were performed with R statistical software packages, and a number of differentially expressed genes (DEGs) were obtained. A functional enrichment analysis was performed for all the DEGs with a BiNGO plug‑in in Cytoscape. Their correlation was analyzed in order to construct a network. The modularity analysis and pathway identification operations were used to identify graph clusters and associated pathways. The underlying molecular mechanisms involving these DEGs were also assessed by data mining. A total of 249 DEGs, which were markedly upregulated and downregulated, were identified. The extracellular region contained the most significantly over‑represented functional terms, with respect to upregulated and downregulated genes, and the closest topological matches were identified for taste transduction and regulation of autophagy. In addition, extracellular matrix‑receptor interactions were identified as the most relevant pathway associated with the progression of GC. The genes for fibronectin 1, secreted phosphoprotein 1, collagen type 4 variant α‑1/2 and thrombospondin 1, which are involved in the pathways, may be considered as potential therapeutic targets for GC. A series of associations between candidate genes and key pathways were also identified for GC, and their correlation may provide novel insights into the pathogenesis of GC.
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Affiliation(s)
- Leilei Guo
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Chunhua Song
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Peng Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Liping Dai
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Jianying Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Kaijuan Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
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170
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Wang S, Tong Y, Ng TB, Lao L, Lam JKW, Zhang KY, Zhang ZJ, Sze SCW. Network pharmacological identification of active compounds and potential actions of Erxian decoction in alleviating menopause-related symptoms. Chin Med 2015; 10:19. [PMID: 26191080 PMCID: PMC4506602 DOI: 10.1186/s13020-015-0051-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 07/01/2015] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Erxian decoction (EXD) is used to treat menopause-related symptoms in Chinese medicine. This study aims to identify the bioactive compounds and potential actions of EXD by network pharmacological analysis. METHODS Two databases, the Traditional Chinese Medicine Systems Pharmacology database and TCM Database@Taiwan, were used to retrieve literature of phytochemicals of EXD. STITCH 4.0 and the Comparative Toxicogenomics Database were used to search for compound-protein and compound-gene interactions, respectively. DAVID Bioinformatics Resources 6.7 and Cytoscape 3.01 with Jepetto plugin software were used to perform a network pharmacological analysis of EXD. RESULTS A total of 721 compounds were identified in EXD, of which 155 exhibited 2,656 compound-protein interactions with 1,963 associated proteins determined by STITCH4.0 database, and of which 210 had 14,893 compound-gene interactions with 8,536 associated genes determined by Comparative Toxicogenomics Database. Sixty three compounds of EXD followed the Lipinski's Rule with OB ≥30% and DL index ≥0.18, of which 20 related to 34 significant pathway- or 12 gene- associated with menopause. CONCLUSIONS Twenty compounds were identified by network pharmacology as potential effective ingredients of EXD for relieving menopause with acceptable oral bioavailability and druggability.
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Affiliation(s)
- Shiwei Wang
- />School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yao Tong
- />School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tzi-Bun Ng
- />School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lixing Lao
- />School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jenny Ka Wing Lam
- />Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kalin Yanbo Zhang
- />School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zhang-Jin Zhang
- />School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Stephen Cho Wing Sze
- />School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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171
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Acosta-Herrera M, Lorenzo-Diaz F, Pino-Yanes M, Corrales A, Valladares F, Klassert TE, Valladares B, Slevogt H, Ma SF, Villar J, Flores C. Lung Transcriptomics during Protective Ventilatory Support in Sepsis-Induced Acute Lung Injury. PLoS One 2015; 10:e0132296. [PMID: 26147972 PMCID: PMC4492998 DOI: 10.1371/journal.pone.0132296] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/11/2015] [Indexed: 01/17/2023] Open
Abstract
Acute lung injury (ALI) is a severe inflammatory process of the lung. The only proven life-saving support is mechanical ventilation (MV) using low tidal volumes (LVT) plus moderate to high levels of positive end-expiratory pressure (PEEP). However, it is currently unknown how they exert the protective effects. To identify the molecular mechanisms modulated by protective MV, this study reports transcriptomic analyses based on microarray and microRNA sequencing in lung tissues from a clinically relevant animal model of sepsis-induced ALI. Sepsis was induced by cecal ligation and puncture (CLP) in male Sprague-Dawley rats. At 24 hours post-CLP, septic animals were randomized to three ventilatory strategies: spontaneous breathing, LVT (6 ml/kg) plus 10 cmH2O PEEP and high tidal volume (HVT, 20 ml/kg) plus 2 cmH2O PEEP. Healthy, non-septic, non-ventilated animals served as controls. After 4 hours of ventilation, lung samples were obtained for histological examination and gene expression analysis using microarray and microRNA sequencing. Validations were assessed using parallel analyses on existing publicly available genome-wide association study findings and transcriptomic human data. The catalogue of deregulated processes differed among experimental groups. The 'response to microorganisms' was the most prominent biological process in septic, non-ventilated and in HVT animals. Unexpectedly, the 'neuron projection morphogenesis' process was one of the most significantly deregulated in LVT. Further support for the key role of the latter process was obtained by microRNA studies, as four species targeting many of its genes (Mir-27a, Mir-103, Mir-17-5p and Mir-130a) were found deregulated. Additional analyses revealed 'VEGF signaling' as a central underlying response mechanism to all the septic groups (spontaneously breathing or mechanically ventilated). Based on this data, we conclude that a co-deregulation of 'VEGF signaling' along with 'neuron projection morphogenesis', which have been never anticipated in ALI pathogenesis, promotes lung-protective effects of LVT with high levels of PEEP.
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Affiliation(s)
- Marialbert Acosta-Herrera
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Fabian Lorenzo-Diaz
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Almudena Corrales
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Francisco Valladares
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Department of Anatomy, Pathology and Histology, University of La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Hortense Slevogt
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Shwu-Fan Ma
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Jesus Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain
- Keenan Research Center for Biomedical Science at the Li KaShing Knowledge Institute, St. Michael´s Hospital, Toronto, Canada
| | - Carlos Flores
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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Glaab E. Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification. Brief Bioinform 2015; 17:440-52. [PMID: 26141830 PMCID: PMC4870394 DOI: 10.1093/bib/bbv044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/27/2022] Open
Abstract
For many complex diseases, an earlier and more reliable diagnosis is considered a key prerequisite for developing more effective therapies to prevent or delay disease progression. Classical statistical learning approaches for specimen classification using omics data, however, often cannot provide diagnostic models with sufficient accuracy and robustness for heterogeneous diseases like cancers or neurodegenerative disorders. In recent years, new approaches for building multivariate biomarker models on omics data have been proposed, which exploit prior biological knowledge from molecular networks and cellular pathways to address these limitations. This survey provides an overview of these recent developments and compares pathway- and network-based specimen classification approaches in terms of their utility for improving model robustness, accuracy and biological interpretability. Different routes to translate omics-based multifactorial biomarker models into clinical diagnostic tests are discussed, and a previous study is presented as example.
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173
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Di Lena P, Martelli PL, Fariselli P, Casadio R. NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. BMC Genomics 2015; 16 Suppl 8:S6. [PMID: 26110971 PMCID: PMC4480278 DOI: 10.1186/1471-2164-16-s8-s6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background Enrichment analysis is a widely applied procedure for shedding light on the molecular mechanisms and functions at the basis of phenotypes, for enlarging the dataset of possibly related genes/proteins and for helping interpretation and prioritization of newly determined variations. Several standard and Network-based enrichment methods are available. Both approaches rely on the annotations that characterize the genes/proteins included in the input set; network based ones also include in different ways physical and functional relationships among different genes or proteins that can be extracted from the available biological networks of interactions. Results Here we describe a novel procedure based on the extraction from the STRING interactome of sub-networks connecting proteins that share the same Gene Ontology(GO) terms for Biological Process (BP). Enrichment analysis is performed by mapping the protein set to be analyzed on the sub-networks, and then by collecting the corresponding annotations. We test the ability of our enrichment method in finding annotation terms disregarded by other enrichment methods available. We benchmarked 244 sets of proteins associated to different Mendelian diseases, according to the OMIM web resource. In 143 cases (58%), the network-based procedure extracts GO terms neglected by the standard method, and in 86 cases (35%), some of the newly enriched GO terms are not included in the set of annotations characterizing the input proteins. We present in detail six cases where our network-based enrichment provides an insight into the biological basis of the diseases, outperforming other freely available network-based methods. Conclusions Considering a set of proteins in the context of their interaction network can help in better defining their functions. Our novel method exploits the information contained in the STRING database for building the minimal connecting network containing all the proteins annotated with the same GO term. The enrichment procedure is performed considering the GO-specific network modules and, when tested on the OMIM-derived benchmark sets, it is able to extract enrichment terms neglected by other methods. Our procedure is effective even when the size of the input protein set is small, requiring at least two input proteins.
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174
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Target deconvolution of bioactive small molecules: the heart of chemical biology and drug discovery. Arch Pharm Res 2015; 38:1627-41. [DOI: 10.1007/s12272-015-0618-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/19/2015] [Indexed: 01/01/2023]
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175
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Wang B, Cunningham JM, Yang XH. Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. Bioinformatics 2015; 31:3043-5. [PMID: 25979472 PMCID: PMC4565027 DOI: 10.1093/bioinformatics/btv289] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/02/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores. It is designed to isolate systematic disturbances and common biological underpinnings from next-generation sequencing (NGS) data. Seq2pathway offers Bioconductor users enhanced capability in discovering collective pathway effects caused by both coding genes and cis-regulation of non-coding elements. AVAILABILITY AND IMPLEMENTATION The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html. CONTACT xyang2@uchicago.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bin Wang
- Section of Hematology/Oncology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - John M Cunningham
- Section of Hematology/Oncology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Xinan Holly Yang
- Section of Hematology/Oncology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA
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176
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Peripheral blood mononuclear cell proteome changes in patients with myelodysplastic syndrome. BIOMED RESEARCH INTERNATIONAL 2015; 2015:872983. [PMID: 25969835 PMCID: PMC4415457 DOI: 10.1155/2015/872983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 03/31/2015] [Indexed: 12/13/2022]
Abstract
Our aim was to search for proteome changes in peripheral blood mononuclear cells (PBMCs) of MDS patients with refractory cytopenia with multilineage dysplasia. PBMCs were isolated from a total of 12 blood samples using a Histopaque-1077 solution. The proteins were fractioned, separated by 2D SDS-PAGE (pI 4–7), and double-stained. The proteomes were compared and statistically processed with Progenesis SameSpots; then proteins were identified by nano-LC-MS/MS. Protein functional association and expression profiles were analyzed using the EnrichNet application and Progenesis SameSpots hierarchical clustering software, respectively. By comparing the cytosolic, membrane, and nuclear fractions of the two groups, 178 significantly (P < 0.05, ANOVA) differing spots were found, corresponding to 139 unique proteins. Data mining of the Reactome and KEGG databases using EnrichNet highlighted the possible involvement of the identified protein alterations in apoptosis, proteasome protein degradation, heat shock protein action, and signal transduction. Western blot analysis revealed underexpression of vinculin and advanced fragmentation of fermitin-3 in MDS patients. To the best of our knowledge, this is the first time that proteome changes have been identified in the mononuclear cells of MDS patients. Vinculin and fermitin-3, the proteins involved in cell adhesion and integrin signaling, have been shown to be dysregulated in MDS.
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177
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Schisler JC, Ronnebaum SM, Madden M, Channell M, Campen M, Willis MS. Endothelial inflammatory transcriptional responses to an altered plasma exposome following inhalation of diesel emissions. Inhal Toxicol 2015; 27:272-80. [PMID: 25942053 DOI: 10.3109/08958378.2015.1030481] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Air pollution, especially emissions derived from traffic sources, is associated with adverse cardiovascular outcomes. However, it remains unclear how inhaled factors drive extrapulmonary pathology. OBJECTIVES Previously, we found that canonical inflammatory response transcripts were elevated in cultured endothelial cells treated with plasma obtained after exposure compared with pre-exposure samples or filtered air (sham) exposures. While the findings confirmed the presence of bioactive factor(s) in the plasma after diesel inhalation, we wanted to better examine the complete genomic response to investigate (1) major responsive transcripts and (2) collected response pathways and ontogeny that may help to refine this method and inform the pathogenesis. METHODS We assayed endothelial RNA with gene expression microarrays, examining the responses of cultured endothelial cells to plasma obtained from six healthy human subjects exposed to 100 μg/m(3) diesel exhaust or filtered air for 2 h on separate occasions. In addition to pre-exposure baseline samples, we investigated samples obtained immediately-post and 24 h-post exposure. RESULTS Microarray analysis of the coronary artery endothelial cells challenged with plasma identified 855 probes that changed over time following diesel exhaust exposure. Over-representation analysis identified inflammatory cytokine pathways were upregulated both at the 2 and 24 h conditions. Novel pathways related to FOXO transcription factors and secreted extracellular factors were also identified in the microarray analysis. CONCLUSIONS These outcomes are consistent with our recent findings that plasma contains bioactive and inflammatory factors following pollutant inhalation and provide a novel pathway to explain the well-reported extrapulmonary toxicity of ambient air pollutants.
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Affiliation(s)
- Jonathan C Schisler
- Department of Pathology and Laboratory Medicine, McAllister Heart Institute, University of North Carolina , Chapel Hill, NC , USA
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178
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Hu G, Wei B, Wang L, Wang L, Kong D, Jin Y, Sun Z. Analysis of gene expression profiles associated with glioma progression. Mol Med Rep 2015; 12:1884-90. [PMID: 25845910 PMCID: PMC4464167 DOI: 10.3892/mmr.2015.3583] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 03/12/2015] [Indexed: 11/13/2022] Open
Abstract
The present study aimed to investigate changes at the transcript level that are associated with spontaneous astrocytoma progression, and further, to discover novel targets for glioma diagnosis and therapy. GSE4290 microarray data downloaded from Gene Expression Omnibus were used to identify the differentially expressed genes (DGEs) by significant analysis of microarray (SAM). The Short Time Series Expression Miner (STEM) method was then applied to class these DEGs based on their degrees of differentiation in the process of tumor progression. Finally, EnrichNet was used to perform the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis based on a protein-protein interaction (PPI) network. A total of 4,506 DEGs were detected, and the number of DEGs was the highest in grade IV cells (2,580 DEGs). These DEGs were classified into nine clusters by the STEM method. In total, 11 KEGG pathways with XD-scores larger than the threshold (0.96) were obtained. The DEGs enriched in pathways 1 (extracellular matrix-receptor interaction), 3 (phagosome) and 6 (type I diabetes mellitus) mainly belonged to cluster 5. Pathway 2 (long-term potentiation), 4 (Vibrio cholerae infection) and 5 (epithelial cell signaling in Helicobacter pylori infection) was involved with DEGs that belonged to different clusters. Significant changes in gene expression occurred during glioma progression. Pathways 1, 3 and 6 may be important for the deterioration of glioma into glioblastoma, and pathways 2, 4 and 5 may have a role at each stage during glioma progression. The associated DEGs, including SV2, NMDAR and mGluRs, may be suitable as biomarkers or therapeutic targets for gliomas.
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Affiliation(s)
- Guozhang Hu
- Department of Emergency Medicine, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bo Wei
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Lina Wang
- Department of Ophthalmology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Le Wang
- Department of Opthalmology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Daliang Kong
- Department of Emergency Medicine, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Ying Jin
- Department of Neurology, Jilin Oilfield General Hospital, Songyuan 131200, P.R. China
| | - Zhigang Sun
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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179
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Frost HR, Li Z, Moore JH. Spectral gene set enrichment (SGSE). BMC Bioinformatics 2015; 16:70. [PMID: 25879888 PMCID: PMC4365810 DOI: 10.1186/s12859-015-0490-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 02/04/2015] [Indexed: 01/29/2023] Open
Abstract
Background Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in the absence of a phenotype variable. Although methods exist for unsupervised gene set testing, they predominantly compute enrichment relative to clusters of the genomic variables with performance strongly dependent on the clustering algorithm and number of clusters. Results We propose a novel method, spectral gene set enrichment (SGSE), for unsupervised competitive testing of the association between gene sets and empirical data sources. SGSE first computes the statistical association between gene sets and principal components (PCs) using our principal component gene set enrichment (PCGSE) method. The overall statistical association between each gene set and the spectral structure of the data is then computed by combining the PC-level p-values using the weighted Z-method with weights set to the PC variance scaled by Tracy-Widom test p-values. Using simulated data, we show that the SGSE algorithm can accurately recover spectral features from noisy data. To illustrate the utility of our method on real data, we demonstrate the superior performance of the SGSE method relative to standard cluster-based techniques for testing the association between MSigDB gene sets and the variance structure of microarray gene expression data. Conclusions Unsupervised gene set testing can provide important information about the biological signal held in high-dimensional genomic data sets. Because it uses the association between gene sets and samples PCs to generate a measure of unsupervised enrichment, the SGSE method is independent of cluster or network creation algorithms and, most importantly, is able to utilize the statistical significance of PC eigenvalues to ignore elements of the data most likely to represent noise. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0490-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- H Robert Frost
- Institute of Quantitative Biomedical Sciences, Geisel School of Medicine, Lebanon, NH, 03756, USA. .,Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Lebanon, NH, 03756, USA. .,Department of Genetics, Dartmouth College, Hanover, NH, 03755, USA.
| | - Zhigang Li
- Institute of Quantitative Biomedical Sciences, Geisel School of Medicine, Lebanon, NH, 03756, USA. .,Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Lebanon, NH, 03756, USA.
| | - Jason H Moore
- Institute of Quantitative Biomedical Sciences, Geisel School of Medicine, Lebanon, NH, 03756, USA. .,Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Lebanon, NH, 03756, USA. .,Department of Genetics, Dartmouth College, Hanover, NH, 03755, USA.
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180
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Belinky F, Nativ N, Stelzer G, Zimmerman S, Iny Stein T, Safran M, Lancet D. PathCards: multi-source consolidation of human biological pathways. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav006. [PMID: 25725062 PMCID: PMC4343183 DOI: 10.1093/database/bav006] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The study of biological pathways is key to a large number of systems analyses. However, many relevant tools consider a limited number of pathway sources, missing out on many genes and gene-to-gene connections. Simply pooling several pathways sources would result in redundancy and the lack of systematic pathway interrelations. To address this, we exercised a combination of hierarchical clustering and nearest neighbor graph representation, with judiciously selected cutoff values, thereby consolidating 3215 human pathways from 12 sources into a set of 1073 SuperPaths. Our unification algorithm finds a balance between reducing redundancy and optimizing the level of pathway-related informativeness for individual genes. We show a substantial enhancement of the SuperPaths’ capacity to infer gene-to-gene relationships when compared with individual pathway sources, separately or taken together. Further, we demonstrate that the chosen 12 sources entail nearly exhaustive gene coverage. The computed SuperPaths are presented in a new online database, PathCards, showing each SuperPath, its constituent network of pathways, and its contained genes. This provides researchers with a rich, searchable systems analysis resource.Database URL:http://pathcards.genecards.org/
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Affiliation(s)
- Frida Belinky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noam Nativ
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gil Stelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shahar Zimmerman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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181
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Laukens K, Naulaerts S, Berghe WV. Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis. Proteomics 2015; 15:981-96. [PMID: 25430566 DOI: 10.1002/pmic.201400296] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/16/2014] [Accepted: 11/24/2014] [Indexed: 12/24/2022]
Abstract
The main result of a great deal of the published proteomics studies is a list of identified proteins, which then needs to be interpreted in relation to the research question and existing knowledge. In the early days of proteomics this interpretation was only based on expert insights, acquired by digesting a large amount of relevant literature. With the growing size and complexity of the experimental datasets, many computational techniques, databases, and tools have claimed a central role in this task. In this review we discuss commonly and less commonly used methods to functionally interpret experimental proteome lists and compare them with available knowledge. We first address several functional analysis and enrichment techniques based on ontologies and literature. Then we outline how various types of network and pathway information can be used. While the problem of functional interpretation of proteome data is to an extent equivalent to the interpretation of transcriptome or other ''omics'' data, this paper addresses some of the specific challenges and solutions of the proteomics field.
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Affiliation(s)
- Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Middelheimlaan, Antwerp, Belgium; Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp / Antwerp University Hospital, Antwerp, Belgium
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182
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Tsuyuzaki K, Morota G, Ishii M, Nakazato T, Miyazaki S, Nikaido I. MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. BMC Bioinformatics 2015; 16:45. [PMID: 25887539 PMCID: PMC4343279 DOI: 10.1186/s12859-015-0453-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 01/08/2015] [Indexed: 11/23/2022] Open
Abstract
Background In genome-wide studies, over-representation analysis (ORA) against a set of genes is an essential step for biological interpretation. Many gene annotation resources and software platforms for ORA have been proposed. Recently, Medical Subject Headings (MeSH) terms, which are annotations of PubMed documents, have been used for ORA. MeSH enables the extraction of broader meaning from the gene lists and is expected to become an exhaustive annotation resource for ORA. However, the existing MeSH ORA software platforms are still not sufficient for several reasons. Results In this work, we developed an original MeSH ORA framework composed of six types of R packages, including MeSH.db, MeSH.AOR.db, MeSH.PCR.db, the org.MeSH.XXX.db-type packages, MeSHDbi, and meshr. Conclusions Using our framework, users can easily conduct MeSH ORA. By utilizing the enriched MeSH terms, related PubMed documents can be retrieved and saved on local machines within this framework. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0453-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Koki Tsuyuzaki
- Department of Medical and Life Science, Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Chiba, Japan. .,Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan.
| | - Gota Morota
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, USA.
| | - Manabu Ishii
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan.
| | - Takeru Nakazato
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), Faculty of Engineering Building 12, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan.
| | - Satoru Miyazaki
- Department of Medical and Life Science, Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Chiba, Japan.
| | - Itoshi Nikaido
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan.
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183
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Kumar M, Sahu SK, Kumar R, Subuddhi A, Maji RK, Jana K, Gupta P, Raffetseder J, Lerm M, Ghosh Z, van Loo G, Beyaert R, Gupta UD, Kundu M, Basu J. MicroRNA let-7 modulates the immune response to Mycobacterium tuberculosis infection via control of A20, an inhibitor of the NF-κB pathway. Cell Host Microbe 2015; 17:345-356. [PMID: 25683052 DOI: 10.1016/j.chom.2015.01.007] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/20/2014] [Accepted: 01/08/2015] [Indexed: 12/31/2022]
Abstract
The outcome of the interaction between Mycobacterium tuberculosis (Mtb) and a macrophage depends on the interplay between host defense and bacterial immune subversion mechanisms. MicroRNAs critically regulate several host defense mechanisms, but their role in the Mtb-macrophage interplay remains unclear. MicroRNA profiling of Mtb-infected macrophages revealed the downregulation of miR-let-7f in a manner dependent on the Mtb secreted effector ESAT-6. We establish that let-7f targets A20, a feedback inhibitor of the NF-κB pathway. Expression of let-7f decreases and A20 increases with progression of Mtb infection in mice. Mtb survival is attenuated in A20-deficient macrophages, and the production of TNF, IL-1β, and nitrite, which are mediators of immunity to Mtb, is correspondingly increased. Further, let-7f overexpression diminishes Mtb survival and augments the production of cytokines including TNF and IL-1β. These results uncover a role for let-7f and its target A20 in regulating immune responses to Mtb and controlling bacterial burden.
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Affiliation(s)
- Manish Kumar
- Department of Chemistry, Bose Institute, Kolkata 700009, India
| | | | - Ranjeet Kumar
- Department of Chemistry, Bose Institute, Kolkata 700009, India
| | | | | | - Kuladip Jana
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Pushpa Gupta
- National Jalma Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282006, India
| | - Johanna Raffetseder
- Division of Microbiology and Molecular Medicine, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, SE-581 85 Linköping, Sweden
| | - Maria Lerm
- Division of Microbiology and Molecular Medicine, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, SE-581 85 Linköping, Sweden
| | - Zhumur Ghosh
- Bioinformatics Centre, Bose Institute, Kolkata 700054, India
| | - Geert van Loo
- VIB Inflammation Research Center, Ghent University, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Rudi Beyaert
- VIB Inflammation Research Center, Ghent University, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Umesh D Gupta
- National Jalma Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282006, India
| | | | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata 700009, India.
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184
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Monti C, Bondi H, Urbani A, Fasano M, Alberio T. Systems biology analysis of the proteomic alterations induced by MPP(+), a Parkinson's disease-related mitochondrial toxin. Front Cell Neurosci 2015; 9:14. [PMID: 25698928 PMCID: PMC4313704 DOI: 10.3389/fncel.2015.00014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/10/2015] [Indexed: 12/21/2022] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease whose etiology has not been completely characterized. Many cellular processes have been proposed to play a role in the neuronal damage and loss: defects in the proteosomal activity, altered protein processing, increased reactive oxygen species burden. Among them, the involvement of a decreased activity and an altered disposal of mitochondria is becoming more and more evident. The mitochondrial toxin 1-methyl-4-phenylpyridinium (MPP(+)), an inhibitor of complex I, has been widely used to reproduce biochemical alterations linked to PD in vitro and its precursor, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine hydrochloride (MPTP), to induce a Parkinson-like syndrome in vivo. Therefore, we performed a meta-analysis of the literature of all the proteomic investigations of neuronal alterations due to MPP(+) treatment and compared it with our results obtained with a mitochondrial proteomic analysis of SH-SY5Y cells treated with MPP(+). By using open-source bioinformatics tools, we identified the biochemical pathways and the molecular functions mostly affected by MPP(+), i.e., ATP production, the mitochondrial unfolded stress response, apoptosis, autophagy, and, most importantly, the synapse funcionality. Eventually, we generated protein networks, based on physical or functional interactions, to highlight the relationships among the molecular actors involved. In particular, we identified the mitochondrial protein HSP60 as the central hub in the protein-protein interaction network. As a whole, this analysis clarified the cellular responses to MPP(+), the specific mitochondrial proteome alterations induced and how this toxic model can recapitulate some pathogenetic events of PD.
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Affiliation(s)
- Chiara Monti
- Biomedical Research Division, Department of Theoretical and Applied Sciences, University of Insubria Busto Arsizio, Italy
| | - Heather Bondi
- Biomedical Research Division, Department of Theoretical and Applied Sciences, University of Insubria Busto Arsizio, Italy ; Center of Neuroscience, University of Insubria Busto Arsizio, Italy
| | - Andrea Urbani
- Santa Lucia IRCCS Foundation Rome, Italy ; Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata," Rome, Italy
| | - Mauro Fasano
- Biomedical Research Division, Department of Theoretical and Applied Sciences, University of Insubria Busto Arsizio, Italy ; Center of Neuroscience, University of Insubria Busto Arsizio, Italy
| | - Tiziana Alberio
- Biomedical Research Division, Department of Theoretical and Applied Sciences, University of Insubria Busto Arsizio, Italy ; Center of Neuroscience, University of Insubria Busto Arsizio, Italy
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185
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Luo X, Yu C, Fu C, Shi W, Wang X, Zeng C, Wang H. Identification of the differentially expressed genes associated with familial combined hyperlipidemia using bioinformatics analysis. Mol Med Rep 2015; 11:4032-8. [PMID: 25625967 PMCID: PMC4394960 DOI: 10.3892/mmr.2015.3263] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 11/18/2014] [Indexed: 12/21/2022] Open
Abstract
The aim of the present study was to screen the differentially expressed genes (DEGs) associated with familial combined hyperlipidemia (FCHL) and examine the changing patterns. The transcription profile of GSE18965 was obtained from the NCBI Gene Expression Omnibus database, including 12 FCHL samples and 12 control specimens. The DEGs were identified using a linear models for microarray data package in the R programming language. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was also performed. Protein-protein interaction (PPI) networks of the DEGs were constructed using the EnrichNet online tool. In addition, cluster analysis of the genes in networks was performed using ClusterONE. A total of 879 DEGs were screened, including 394 upregulated and 485 downregulated genes. Enrichment analysis identified four important KEGG pathways associated with FCHL: One carbon pool by folate, α-linolenic acid metabolism, asthma and the glycosphingolipid biosynthesis-globo series. GO annotation identified 12 enriched biological processes, including one associated with hematopoiesis and four associated with bone cell differentiation. This identification was in accordance with clinical data and experiments into hyperlipidemia and bone lesions. Based on PPI networks, these DEGs had a close association with immune responses, hormone responses and cytokine-cytokine receptors. In conclusion, these DEGs may be used as specific therapeutic molecular targets in the treatment of FCHL. The present findings may provide the basis for understanding the pathogenesis of FCHL in future studies. However, further experiments are required to confirm these results.
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Affiliation(s)
- Xiaoli Luo
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing Institute of Cardiology, Chongqing 400042, P.R. China
| | - Changqing Yu
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing Institute of Cardiology, Chongqing 400042, P.R. China
| | - Chunjiang Fu
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing Institute of Cardiology, Chongqing 400042, P.R. China
| | - Weibin Shi
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing Institute of Cardiology, Chongqing 400042, P.R. China
| | - Xukai Wang
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing Institute of Cardiology, Chongqing 400042, P.R. China
| | - Chunyu Zeng
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing Institute of Cardiology, Chongqing 400042, P.R. China
| | - Hongyong Wang
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing Institute of Cardiology, Chongqing 400042, P.R. China
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186
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Glaab E, Schneider R. Comparative pathway and network analysis of brain transcriptome changes during adult aging and in Parkinson's disease. Neurobiol Dis 2014; 74:1-13. [PMID: 25447234 DOI: 10.1016/j.nbd.2014.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/23/2014] [Accepted: 11/03/2014] [Indexed: 01/19/2023] Open
Abstract
Aging is considered as one of the main factors promoting the risk for Parkinson's disease (PD), and common mechanisms of dopamine neuron degeneration in aging and PD have been proposed in recent years. Here, we use a statistical meta-analysis of human brain transcriptomics data to investigate potential mechanistic relationships between adult brain aging and PD pathogenesis at the pathway and network level. The analyses identify statistically significant shared pathway and network alterations in aging and PD and an enrichment in PD-associated sequence variants from genome-wide association studies among the jointly deregulated genes. We find robust discriminative patterns for groups of functionally related genes with potential applications as combined risk biomarkers to detect aging- and PD-linked oxidative stress, e.g., a consistent over-expression of metallothioneins matching with findings in previous independent studies. Interestingly, analyzing the regulatory network and mouse knockout expression data for NR4A2, a transcription factor previously associated with rare mutations in PD and here found as the most significantly under-expressed gene in PD among the jointly altered genes, suggests that aging-related NR4A2 expression changes may increase PD risk via downstream effects similar to disease-linked mutations and to expression changes in sporadic PD. Overall, the analyses suggest mechanistic explanations for the age-dependence of PD risk and reveal significant and robust shared process alterations with potential applications in biomarker development for pre-symptomatic risk assessment or early stage diagnosis.
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Affiliation(s)
- Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg.
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
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187
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Chen J, Sun M, Shen B. Deciphering oncogenic drivers: from single genes to integrated pathways. Brief Bioinform 2014; 16:413-28. [PMID: 25378434 DOI: 10.1093/bib/bbu039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
Technological advances in next-generation sequencing have uncovered a wide spectrum of aberrations in cancer genomes. The extreme diversity in cancer mutations necessitates computational approaches to differentiate between the 'drivers' with vital function in cancer progression and those nonfunctional 'passengers'. Although individual driver mutations are routinely identified, mutational profiles of different tumors are highly heterogeneous. There is growing consensus that pathways rather than single genes are the primary target of mutations. Here we review extant bioinformatics approaches to identifying oncogenic drivers at different mutational levels, highlighting the strategies for discovering driver pathways and networks from cancer mutation data. These approaches will help reduce the mutation complexity, thus providing a simplified picture of cancer.
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188
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Ibrahim M, Jassim S, Cawthorne MA, Langlands K. A MATLAB tool for pathway enrichment using a topology-based pathway regulation score. BMC Bioinformatics 2014; 15:358. [PMID: 25367050 PMCID: PMC4255424 DOI: 10.1186/s12859-014-0358-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/22/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn. For example, a range of traditional statistical and computational pathway analysis approaches have been used to identify over-represented processes in microarray data derived from various disease states. However, most of these approaches tend not to exploit the full spectrum of gene expression data, or the various relationships and dependencies. Previously, we described a pathway enrichment analysis tool created in MATLAB that yields a Pathway Regulation Score (PRS) by considering signalling pathway topology, and the overrepresentation and magnitude of differentially-expressed genes (J Comput Biol 19:563-573, 2012). Herein, we extended this approach to include metabolic pathways, and described the use of a graphical user interface (GUI). RESULTS Using input from a variety of microarray platforms and species, users are able to calculate PRS scores, along with a corresponding z-score for comparison. Further pathway significance assessment may be performed to increase confidence in the pathways obtained, and users can view Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway diagrams marked-up to highlight impacted genes. CONCLUSIONS The PRS tool provides a filter in the isolation of biologically-relevant insights from complex transcriptomic data.
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Affiliation(s)
- Maysson Ibrahim
- Department of Applied Computing, the University of Buckingham, Buckingham, MK18 1EG, UK. .,The Buckingham Institute for Translational Medicine, the University of Buckingham, Buckingham, MK18 1EG, UK.
| | - Sabah Jassim
- Department of Applied Computing, the University of Buckingham, Buckingham, MK18 1EG, UK.
| | - Michael Anthony Cawthorne
- The Buckingham Institute for Translational Medicine, the University of Buckingham, Buckingham, MK18 1EG, UK.
| | - Kenneth Langlands
- The Buckingham Institute for Translational Medicine, the University of Buckingham, Buckingham, MK18 1EG, UK.
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189
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Taha K. Determining Semantically Related Significant Genes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:1119-1130. [PMID: 26357049 DOI: 10.1109/tcbb.2014.2344668] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
GO relation embodies some aspects of existence dependency. If GO term xis existence-dependent on GO term y, the presence of y implies the presence of x. Therefore, the genes annotated with the function of the GO term y are usually functionally and semantically related to the genes annotated with the function of the GO term x. A large number of gene set enrichment analysis methods have been developed in recent years for analyzing gene sets enrichment. However, most of these methods overlook the structural dependencies between GO terms in GO graph by not considering the concept of existence dependency. We propose in this paper a biological search engine called RSGSearch that identifies enriched sets of genes annotated with different functions using the concept of existence dependency. We observe that GO term xcannot be existence-dependent on GO term y, if x- and y- have the same specificity (biological characteristics). After encoding into a numeric format the contributions of GO terms annotating target genes to the semantics of their lowest common ancestors (LCAs), RSGSearch uses microarray experiment to identify the most significant LCA that annotates the result genes. We evaluated RSGSearch experimentally and compared it with five gene set enrichment systems. Results showed marked improvement.
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190
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Taha K. RGFinder: a system for determining semantically related genes using GO graph minimum spanning tree. IEEE Trans Nanobioscience 2014; 14:24-37. [PMID: 25343765 DOI: 10.1109/tnb.2014.2363295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Biologists often need to know the set S' of genes that are the most functionally and semantically related to a given set S of genes. For determining the set S', most current gene similarity measures overlook the structural dependencies among the Gene Ontology (GO) terms annotating the set S, which may lead to erroneous results. We introduce in this paper a biological search engine called RGFinder that considers the structural dependencies among GO terms by employing the concept of existence dependency. RGFinder assigns a weight to each edge in GO graph to represent the degree of relatedness between the two GO terms connected by the edge. The value of the weight is determined based on the following factors: 1) type of the relation represented by the edge (e.g., an "is-a" relation is assigned a different weight than a "part-of" relation), 2) the functional relationship between the two GO terms connected by the edge, and 3) the string-substring relationship between the names of the two GO terms connected by the edge. RGFinder then constructs a minimum spanning tree of GO graph based on these weights. In the framework of RGFinder, the set S' is annotated to the GO terms located at the lowest convergences of the subtree of the minimum spanning tree that passes through the GO terms annotating set S. We evaluated RGFinder experimentally and compared it with four gene set enrichment systems. Results showed marked improvement.
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191
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Wu M, Kwoh CK, Li X, Zheng J. Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. BMC SYSTEMS BIOLOGY 2014; 8:107. [PMID: 25208583 PMCID: PMC4236725 DOI: 10.1186/s12918-014-0107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 07/11/2014] [Indexed: 11/18/2022]
Abstract
Background The regulatory mechanism of recombination is one of the most fundamental problems in genomics, with wide applications in genome wide association studies (GWAS), birth-defect diseases, molecular evolution, cancer research, etc. Recombination events cluster into short genomic regions called “recombination hotspots”. Recently, a zinc finger protein PRDM9 was reported to regulate recombination hotspots in human and mouse genomes. In addition, a 13-mer motif contained in the binding sites of PRDM9 is found to be enriched in human hotspots. However, this 13-mer motif only covers a fraction of hotspots, indicating that PRDM9 is not the only regulator of recombination hotspots. Therefore, the challenge of discovering other regulators of recombination hotspots becomes significant. Furthermore, recombination is a complex process. Hence, multiple proteins acting as machinery, rather than individual proteins, are more likely to carry out this process in a precise and stable manner. Therefore, the extension of the prediction of individual trans-regulators to protein complexes is also highly desired. Results In this paper, we introduce a pipeline to identify genes and protein complexes associated with recombination hotspots. First, we prioritize proteins associated with hotspots based on their preference of binding to hotspots and coldspots. Second, using the above identified genes as seeds, we apply the Random Walk with Restart algorithm (RWR) to propagate their influences to other proteins in protein-protein interaction (PPI) networks. Hence, many proteins without DNA-binding information will also be assigned a score to implicate their roles in recombination hotspots. Third, we construct sub-PPI networks induced by top genes ranked by RWR for various species (e.g., yeast, human and mouse) and detect protein complexes in those sub-PPI networks. Conclusions The GO term analysis show that our prioritizing methods and the RWR algorithm are capable of identifying novel genes associated with recombination hotspots. The trans-regulators predicted by our pipeline are enriched with epigenetic functions (e.g., histone modifications), demonstrating the epigenetic regulatory mechanisms of recombination hotspots. The identified protein complexes also provide us with candidates to further investigate the molecular machineries for recombination hotspots. Moreover, the experimental data and results are available on our web site http://www.ntu.edu.sg/home/zhengjie/data/RecombinationHotspot/NetPipe/.
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192
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Cornish AJ, Markowetz F. SANTA: quantifying the functional content of molecular networks. PLoS Comput Biol 2014; 10:e1003808. [PMID: 25210953 PMCID: PMC4161294 DOI: 10.1371/journal.pcbi.1003808] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 07/15/2014] [Indexed: 12/31/2022] Open
Abstract
Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functional content of molecular networks. Based on the guilt-by-association principle, our approach (called SANTA) quantifies the strength of association between a gene set and a network, and functionally annotates molecular networks like other enrichment methods annotate lists of genes. As a general association measure, SANTA can (i) functionally annotate experimentally derived networks using a collection of curated gene sets and (ii) annotate experimentally derived gene sets using a collection of curated networks, as well as (iii) prioritize genes for follow-up analyses. We exemplify the efficacy of SANTA in several case studies using the S. cerevisiae genetic interaction network and genome-wide RNAi screens in cancer cell lines. Our theory, simulations, and applications show that SANTA provides a principled statistical way to quantify the association between molecular networks and cellular functions and phenotypes. SANTA is available from http://bioconductor.org/packages/release/bioc/html/SANTA.html.
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Affiliation(s)
- Alex J. Cornish
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
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193
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Mooney MA, Nigg JT, McWeeney SK, Wilmot B. Functional and genomic context in pathway analysis of GWAS data. Trends Genet 2014; 30:390-400. [PMID: 25154796 DOI: 10.1016/j.tig.2014.07.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/18/2014] [Accepted: 07/18/2014] [Indexed: 02/07/2023]
Abstract
Gene set analysis (GSA) is a promising tool for uncovering the polygenic effects associated with complex diseases. However, the available techniques reflect a wide variety of hypotheses about how genetic effects interact to contribute to disease susceptibility. The lack of consensus about the best way to perform GSA has led to confusion in the field and has made it difficult to compare results across methods. A clear understanding of the various choices made during GSA - such as how gene sets are defined, how single-nucleotide polymorphisms (SNPs) are assigned to genes, and how individual SNP-level effects are aggregated to produce gene- or pathway-level effects - will improve the interpretability and comparability of results across methods and studies. In this review we provide an overview of the various data sources used to construct gene sets and the statistical methods used to test for gene set association, as well as provide guidelines for ensuring the comparability of results.
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Affiliation(s)
- Michael A Mooney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; OHSU Knight Cancer Institute, Portland, OR, USA
| | - Joel T Nigg
- Division of Psychology, Department of Psychiatry, Oregon Health & Science University, Portland, OR, USA; Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Portland, OR, USA; OHSU Knight Cancer Institute, Portland, OR, USA.
| | - Beth Wilmot
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Portland, OR, USA; OHSU Knight Cancer Institute, Portland, OR, USA
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194
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Natale M, Benso A, Di Carlo S, Ficarra E. FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks. GENOMICS, PROTEOMICS & BIOINFORMATICS 2014; 12:178-86. [PMID: 25153667 PMCID: PMC4411368 DOI: 10.1016/j.gpb.2014.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/15/2014] [Accepted: 05/30/2014] [Indexed: 01/04/2023]
Abstract
The characterization of the interacting behaviors of complex biological systems is a primary objective in protein-protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected protein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in diseases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.
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Affiliation(s)
- Massimo Natale
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy.
| | - Alfredo Benso
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy
| | - Stefano Di Carlo
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy
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195
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Zhang H, Wang F, Xu H, Liu Y, Liu J, Zhao H, Gelernter J. Differentially co-expressed genes in postmortem prefrontal cortex of individuals with alcohol use disorders: influence on alcohol metabolism-related pathways. Hum Genet 2014; 133:1383-94. [PMID: 25073604 DOI: 10.1007/s00439-014-1473-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/18/2014] [Indexed: 01/01/2023]
Abstract
Chronic alcohol consumption may induce gene expression alterations in brain reward regions such as the prefrontal cortex (PFC), modulating the risk of alcohol use disorders (AUDs). Transcriptome profiles of 23 AUD cases and 23 matched controls (16 pairs of males and 7 pairs of females) in postmortem PFC were generated using Illumina's HumanHT-12 v4 Expression BeadChip. Probe-level differentially expressed genes and gene modules in AUD subjects were identified using multiple linear regression and weighted gene co-expression network analyses. The enrichment of differentially co-expressed genes in alcohol dependence-associated genes identified by genome-wide association studies (GWAS) was examined using gene set enrichment analysis. Biological pathways overrepresented by differentially co-expressed genes were uncovered using DAVID bioinformatics resources. Three AUD-associated gene modules in males [Module 1 (561 probes mapping to 505 genes): r = 0.42, P(correlation) = 0.020; Module 2 (815 probes mapping to 713 genes): r = 0.41, P(correlation) = 0.020; Module 3 (1,446 probes mapping to 1,305 genes): r = -0.38, P(correlation) = 0.030] and one AUD-associated gene module in females [Module 4 (683 probes mapping to 652 genes): r = 0.64, P(correlation) = 0.010] were identified. Differentially expressed genes mapped by significant expression probes (P(nominal) ≤ 0.05) clustered in Modules 1 and 2 were enriched in GWAS-identified alcohol dependence-associated genes [Module 1 (134 genes): P = 0.028; Module 2 (243 genes): P = 0.004]. These differentially expressed genes, including ALDH2, ALDH7A1, and ALDH9A1, are involved in cellular functions such as aldehyde detoxification, mitochondrial function, and fatty acid metabolism. Our study revealed differentially co-expressed genes in postmortem PFC of AUD subjects and demonstrated that some of these differentially co-expressed genes participate in alcohol metabolism.
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Affiliation(s)
- Huiping Zhang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA,
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196
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Rauniyar N, Gupta V, Balch WE, Yates JR. Quantitative proteomic profiling reveals differentially regulated proteins in cystic fibrosis cells. J Proteome Res 2014; 13:4668-75. [PMID: 24818864 PMCID: PMC4224989 DOI: 10.1021/pr500370g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The
most prevalent cause of cystic fibrosis (CF) is the deletion
of a phenylalanine residue at position 508 in CFTR (ΔF508-CFTR)
protein. The mutated protein fails to fold properly, is retained in
the endoplasmic reticulum via the action of molecular chaperones,
and is tagged for degradation. In this study, the differences in protein
expression levels in CF cell models were assessed using a systems
biology approach aided by the sensitivity of MudPIT proteomics. Analysis
of the differential proteome modulation without a priori hypotheses
has the potential to identify markers that have not yet been documented.
These may also serve as the basis for developing new diagnostic and
treatment modalities for CF. Several novel differentially expressed
proteins observed in our study are likely to play important roles
in the pathogenesis of CF and may serve as a useful resource for the
CF scientific community.
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Affiliation(s)
- Navin Rauniyar
- Department of Chemical Physiology, ‡Department of Cell and Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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197
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Landesfeind M, Kaever A, Feussner K, Thurow C, Gatz C, Feussner I, Meinicke P. Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software. PeerJ 2014; 2:e239. [PMID: 24688832 PMCID: PMC3961162 DOI: 10.7717/peerj.239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 12/17/2013] [Indexed: 11/20/2022] Open
Abstract
State of the art high-throughput technologies allow comprehensive experimental studies of organism metabolism and induce the need for a convenient presentation of large heterogeneous datasets. Especially, the combined analysis and visualization of data from different high-throughput technologies remains a key challenge in bioinformatics. We present here the MarVis-Graph software for integrative analysis of metabolic and transcriptomic data. All experimental data is investigated in terms of the full metabolic network obtained from a reference database. The reactions of the network are scored based on the associated data, and sub-networks, according to connected high-scoring reactions, are identified. Finally, MarVis-Graph scores the detected sub-networks, evaluates them by means of a random permutation test and presents them as a ranked list. Furthermore, MarVis-Graph features an interactive network visualization that provides researchers with a convenient view on the results. The key advantage of MarVis-Graph is the analysis of reactions detached from their pathways so that it is possible to identify new pathways or to connect known pathways by previously unrelated reactions. The MarVis-Graph software is freely available for academic use and can be downloaded at: http://marvis.gobics.de/marvis-graph.
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Affiliation(s)
- Manuel Landesfeind
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University , Göttingen , Germany
| | - Alexander Kaever
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University , Göttingen , Germany
| | - Kirstin Feussner
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University , Göttingen , Germany
| | - Corinna Thurow
- Department for Plant Molecular Biology and Physiology, Schwann-Schleiden-Research-Center for Molecular Cell Biology, Georg-August-University , Göttingen , Germany
| | - Christiane Gatz
- Department for Plant Molecular Biology and Physiology, Schwann-Schleiden-Research-Center for Molecular Cell Biology, Georg-August-University , Göttingen , Germany
| | - Ivo Feussner
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University , Göttingen , Germany
| | - Peter Meinicke
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University , Göttingen , Germany
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198
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Abstract
Most biochemical reactions in a cell are regulated by highly specialized proteins, which are the prime mediators of the cellular phenotype. Therefore the identification, quantitation and characterization of all proteins in a cell are of utmost importance to understand the molecular processes that mediate cellular physiology. With the advent of robust and reliable mass spectrometers that are able to analyze complex protein mixtures within a reasonable timeframe, the systematic analysis of all proteins in a cell becomes feasible. Besides the ongoing improvements of analytical hardware, standardized methods to analyze and study all proteins have to be developed that allow the generation of testable new hypothesis based on the enormous pre-existing amount of biological information. Here we discuss current strategies on how to gather, filter and analyze proteomic data sates using available software packages.
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199
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Abstract
The rise of systems biology is intertwined with that of genomics, yet their primordial relationship to one another is ill-defined. We discuss how the growth of genomics provided a critical boost to the popularity of systems biology. We describe the parts of genomics that share common areas of interest with systems biology today in the areas of gene expression, network inference, chromatin state analysis, pathway analysis, personalized medicine, and upcoming areas of synergy as genomics continues to expand its scope across all biomedical fields.
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Affiliation(s)
- Ana Conesa
- Genomics of Gene Expression Lab, Centro de Investigaciones Príncipe Felipe, Valencia, Spain
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
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200
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Winterhalter C, Widera P, Krasnogor N. JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks. ACTA ACUST UNITED AC 2013; 30:1029-30. [PMID: 24363376 PMCID: PMC3967109 DOI: 10.1093/bioinformatics/btt732] [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] [Indexed: 12/03/2022]
Abstract
Summary: JEPETTO (Java Enrichment of Pathways Extended To TOpology) is a Cytoscape 3.x plugin performing integrative human gene set analysis. It identifies functional associations between genes and known cellular pathways, and processes using protein interaction networks and topological analysis. The plugin integrates information from three separate web servers we published previously, specializing in enrichment analysis, pathways expansion and topological matching. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. We demonstrate the utility of the JEPETTO plugin on a set of misregulated genes associated with Alzheimer’s disease. Availability: Source code and binaries are freely available for download at http://apps.cytoscape.org/apps/jepetto, implemented in Java and multi-platform. Installable directly via Cytoscape plugin manager. Released under the GNU General Public Licence. Contact:jepetto.plugin@gmail.com Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Charles Winterhalter
- Institute of Systems & Synthetic Biology, University of Evry Val-d'Essonne, 91000 Evry, France and School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK
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