Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Nucleic Acids Research - Tập 37 Số 1 - Trang 1-13 - 2009
Da Wei Huang1, Brad T. Sherman1, Richard A. Lempicki1
1Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC-Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD, 21702, USA

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Ashburner, 2000, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat. Genet., 25, 25, 10.1038/75556

Khatri, 2002, Profiling gene expression using onto-express, Genomics, 79, 266, 10.1006/geno.2002.6698

Robinson, 2002, FunSpec: a web-based cluster interpreter for yeast, BMC Bioinformatics, 3, 35, 10.1186/1471-2105-3-35

Berriz, 2003, Characterizing gene sets with FuncAssociate, Bioinformatics, 19, 2502, 10.1093/bioinformatics/btg363

Castillo-Davis, 2003, GeneMerge—post-genomic analysis, data mining, and hypothesis testing, Bioinformatics, 19, 891, 10.1093/bioinformatics/btg114

Dennis, 2003, DAVID: Database for Annotation, Visualization, and Integrated Discovery, Genome Biol., 4, P3, 10.1186/gb-2003-4-5-p3

Doniger, 2003, MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data, Genome Biol., 4, R7, 10.1186/gb-2003-4-1-r7

Hosack, 2003, Identifying biological themes within lists of genes with EASE, Genome Biol., 4, R70, 10.1186/gb-2003-4-10-r70

Martinez-Cruz, 2003, GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data, Bioinformatics, 19, 2158, 10.1093/bioinformatics/btg291

Zeeberg, 2003, GoMiner: a resource for biological interpretation of genomic and proteomic data, Genome Biol., 4, R28, 10.1186/gb-2003-4-4-r28

Curtis, 2005, Pathways to the analysis of microarray data, Trends Biotechnol., 23, 429, 10.1016/j.tibtech.2005.05.011

Khatri, 2005, Ontological analysis of gene expression data: current tools, limitations, and open problems, Bioinformatics, 21, 3587, 10.1093/bioinformatics/bti565

Al-Shahrour, 2004, FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes, Bioinformatics, 20, 578, 10.1093/bioinformatics/btg455

Beissbarth, 2004, GOstat: find statistically overrepresented Gene Ontologies within a group of genes, Bioinformatics, 20, 1464, 10.1093/bioinformatics/bth088

Boyle, 2004, GO::TermFinder–open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes, Bioinformatics, 20, 3710, 10.1093/bioinformatics/bth456

Breitling, 2004, Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments, BMC Bioinformatics, 5, 34, 10.1186/1471-2105-5-34

Breslin, 2004, Comparing functional annotation analyses with Catmap, BMC Bioinformatics, 5, 193, 10.1186/1471-2105-5-193

Martin, 2004, GOToolBox: functional analysis of gene datasets based on Gene Ontology, Genome Biol., 5, R101, 10.1186/gb-2004-5-12-r101

Masseroli, 2004, GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining, Nucleic Acids Res., 32, W293, 10.1093/nar/gkh432

Pasquier, 2004, THEA: ontology-driven analysis of microarray data, Bioinformatics, 20, 2636, 10.1093/bioinformatics/bth295

Shah, 2004, CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology, Bioinformatics, 20, 1196, 10.1093/bioinformatics/bth056

Smid, 2004, GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms, Bioinformatics, 20, 2618, 10.1093/bioinformatics/bth293

Volinia, 2004, GOAL: automated Gene Ontology analysis of expression profiles, Nucleic Acids Res., 32, W492, 10.1093/nar/gkh443

Zhang, 2004, GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies, BMC Bioinformatics, 5, 16, 10.1186/1471-2105-5-16

Zhong, 2004, GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space, Appl. Bioinformatics, 3, 261, 10.2165/00822942-200403040-00009

Al-Shahrour, 2005, BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments, Nucleic Acids Res., 33, W460, 10.1093/nar/gki456

Bluthgen, 2005, Biological profiling of gene groups utilizing Gene Ontology, Genome Inform., 16, 106

Boorsma, 2005, T-profiler: scoring the activity of predefined groups of genes using gene expression data, Nucleic Acids Res., 33, W592, 10.1093/nar/gki484

Kim, 2005, PAGE: parametric analysis of gene set enrichment, BMC Bioinformatics, 6, 144, 10.1186/1471-2105-6-144

Kokocinski, 2005, FACT–a framework for the functional interpretation of high-throughput experiments, BMC Bioinformatics, 6, 161, 10.1186/1471-2105-6-161

Lee, 2005, ErmineJ: tool for functional analysis of gene expression data sets, BMC Bioinformatics, 6, 269, 10.1186/1471-2105-6-269

Lee, 2005, GObar: a gene ontology based analysis and visualization tool for gene sets, BMC Bioinformatics, 6, 189, 10.1186/1471-2105-6-189

Maere, 2005, BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks, Bioinformatics, 21, 3448, 10.1093/bioinformatics/bti551

Newman, 2005, L2L: a simple tool for discovering the hidden significance in microarray expression data, Genome Biol., 6, R81, 10.1186/gb-2005-6-9-r81

Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl Acad. Sci. USA, 102, 15545, 10.1073/pnas.0506580102

Tu, 2005, MEGO: gene functional module expression based on gene ontology, Biotechniques, 38, 277, 10.2144/05382RR04

Wrobel, 2005, goCluster integrates statistical analysis and functional interpretation of microarray expression data, Bioinformatics, 21, 3575, 10.1093/bioinformatics/bti574

Young, 2005, OntologyTraverser: an R package for GO analysis, Bioinformatics, 21, 275, 10.1093/bioinformatics/bth495

Zeeberg, 2005, High-throughput GoMiner, an ‘industrial-strength’ integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID), BMC Bioinformatics, 6, 168, 10.1186/1471-2105-6-168

Zhang, 2005, WebGestalt: an integrated system for exploring gene sets in various biological contexts, Nucleic Acids Res., 33, W741, 10.1093/nar/gki475

Alexa, 2006, Improved scoring of functional groups from gene expression data by decorrelating GO graph structure, Bioinformatics, 22, 1600, 10.1093/bioinformatics/btl140

Beisvag, 2006, GeneTools—application for functional annotation and statistical hypothesis testing, BMC Bioinformatics, 7, 470, 10.1186/1471-2105-7-470

Henegar, 2006, Clustering biological annotations and gene expression data to identify putatively co-regulated biological processes, J. Bioinform. Comput. Biol., 4, 833, 10.1142/S0219720006002181

Lewin, 2006, Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data, BMC Bioinformatics, 7, 426, 10.1186/1471-2105-7-426

Nam, 2006, ADGO: analysis of differentially expressed gene sets using composite GO annotation, Bioinformatics, 22, 2249, 10.1093/bioinformatics/btl378

Pereira, 2006, Gene class expression: analysis tool of Gene Ontology terms with gene expression data, Genet. Mol. Res., 5, 108

Rubin, 2006, Circumventing the cut-off for enrichment analysis, Brief Bioinform., 7, 202, 10.1093/bib/bbl013

Scheer, 2006, JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information, Nucleic Acids Res., 34, W510, 10.1093/nar/gkl329

Sealfon, 2006, GOLEM: an interactive graph-based gene-ontology navigation and analysis tool, BMC Bioinformatics, 7, 443, 10.1186/1471-2105-7-443

Sun, 2006, GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology tool for analysis of genomic and proteomic data, BMC Bioinformatics, 7, S23, 10.1186/1471-2105-7-S2-S23

Usadel, 2006, PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments, BMC Bioinformatics, 7, 535, 10.1186/1471-2105-7-535

Vencio, 2006, BayGO: Bayesian analysis of ontology term enrichment in microarray data, BMC Bioinformatics, 7, 86, 10.1186/1471-2105-7-86

Verspoor, 2006, A categorization approach to automated ontological function annotation, Protein Sci., 15, 1544, 10.1110/ps.062184006

Ye, 2006, WEGO: a web tool for plotting GO annotations, Nucleic Acids Res., 34, W293, 10.1093/nar/gkl031

Al-Shahrour, 2007, From genes to functional classes in the study of biological systems, BMC Bioinformatics, 8, 114, 10.1186/1471-2105-8-114

Al-Shahrour, 2007, FatiGO + : a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments, Nucleic Acids Res., 35, W91, 10.1093/nar/gkm260

Backes, 2007, GeneTrail—advanced gene set enrichment analysis, Nucleic Acids Res., 35, W186, 10.1093/nar/gkm323

Blom, 2007, FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes, Bioinformatics, 23, 1161, 10.1093/bioinformatics/btl658

Carmona-Saez, 2007, GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists, Genome Biol., 8, R3, 10.1186/gb-2007-8-1-r3

Huang da, 2007, The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists, Genome Biol., 8, R183, 10.1186/gb-2007-8-9-r183

Huang da, 2007, DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists, Nucleic Acids Res., 35, W169, 10.1093/nar/gkm415

Khatri, 2007, Onto-Tools: new additions and improvements in 2006, Nucleic Acids Res., 35, W206, 10.1093/nar/gkm327

Kim, 2007, GAzer: gene set analyzer, Bioinformatics, 23, 1697, 10.1093/bioinformatics/btm144

Reimand, 2007, g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments, Nucleic Acids Res., 35, W193, 10.1093/nar/gkm226

Sherman, 2007, DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis, BMC Bioinformatics, 8, 426, 10.1186/1471-2105-8-426

Zhou, 2007, EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species, BMC Genomics, 8, 246, 10.1186/1471-2164-8-246

Alibes, 2008, PaLS: filtering common literature, biological terms and pathway information, Nucleic Acids Res., 36, W364, 10.1093/nar/gkn251

Antonov, 2008, ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data, Nucleic Acids Res., 36, W347, 10.1093/nar/gkn239

Bauer, 2008, Ontologizer 2.0 - A multifunctional tool for GO term enrichment analysis and data exploration, Bioinformatics., 24, 1650, 10.1093/bioinformatics/btn250

Zheng, 2008, GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis, Nucleic Acids Res., 36, W358, 10.1093/nar/gkn276

Frohlich, 2007, GOSim—an R-package for computation of information theoretic GO similarities between terms and gene products, BMC Bioinformatics, 8, 166, 10.1186/1471-2105-8-166

Zhu, 2007, GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology, BMC Genomics, 8, 30, 10.1186/1471-2164-8-30

Vencio, 2007, ProbCD: enrichment analysis accounting for categorization uncertainty, BMC Bioinformatics, 8, 383, 10.1186/1471-2105-8-383

Mosquera, 2008, SerbGO: searching for the best GO tool, Nucleic Acids Res., 36, W368, 10.1093/nar/gkn256

Rhee, 2008, Use and misuse of the gene ontology annotations, Nat. Rev. Genet., 9, 509, 10.1038/nrg2363

Rivals, 2007, Enrichment or depletion of a GO category within a class of genes: which test?, Bioinformatics, 23, 401, 10.1093/bioinformatics/btl633

Nilsson, 2007, Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies, Genome Biol., 8, R74, 10.1186/gb-2007-8-5-r74

Yang, 2008, Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories, Bioinformatics, 24, 265, 10.1093/bioinformatics/btm558

Jiang, 2007, Extensions to gene set enrichment, Bioinformatics, 23, 306, 10.1093/bioinformatics/btl599

Goeman, 2007, Analyzing gene expression data in terms of gene sets: methodological issues, Bioinformatics, 23, 980, 10.1093/bioinformatics/btm051

Gold, 2007, Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL, Brief Bioinform., 8, 71, 10.1093/bib/bbl019

Huang, 2008, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 10.1038/nprot.2008.211

Joslyn, 2004, The gene ontology categorizer, Bioinformatics, 20, i169, 10.1093/bioinformatics/bth921

Barriot, 2007, How to decide which are the most pertinent overly-represented features during gene set enrichment analysis, BMC Bioinformatics, 8, 332, 10.1186/1471-2105-8-332

Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. B, 57, 289

Dudoit, 2003, Multiple hypothesis testing in microarray experiments, Stat. Sci., 18, 71, 10.1214/ss/1056397487

Draghici, 2006, Babel's tower revisited: a universal resource for cross-referencing across annotation databases, Bioinformatics, 22, 2934, 10.1093/bioinformatics/btl372

Kirov, 2005, GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments, BMC Bioinformatics, 6, 72, 10.1186/1471-2105-6-72

Maglott, 2007, Entrez Gene: gene-centered information at NCBI, Nucleic Acids Res., 35, D26, 10.1093/nar/gkl993

The UniProt Consortium, 2008, The universal protein resource (UniProt), Nucleic Acids Res., 36, D190, 10.1093/nar/gkm895

Wu, 2003, The protein information resource, Nucleic Acids Res., 31, 345, 10.1093/nar/gkg040

Bussey, 2003, MatchMiner: a tool for batch navigation among gene and gene product identifiers, Genome Biol., 4, R27, 10.1186/gb-2003-4-4-r27

Alibes, 2007, IDconverter and IDClight: conversion and annotation of gene and protein IDs, BMC Bioinformatics, 8, 9, 10.1186/1471-2105-8-9