Crossref journal-article
Oxford University Press (OUP)
Nucleic Acids Research (286)
Bibliography

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2008). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37(1), 1–13.

Authors 3
  1. Da Wei Huang (first)
  2. Brad T. Sherman (additional)
  3. Richard A. Lempicki (additional)
References 93 Referenced 12,138
  1. 10.1038/75556 / Nat. Genet. / Gene ontology: tool for the unification of biology. The Gene Ontology Consortium by Ashburner (2000)
  2. 10.1006/geno.2002.6698 / Genomics / Profiling gene expression using onto-express by Khatri (2002)
  3. 10.1186/1471-2105-3-35 / BMC Bioinformatics / FunSpec: a web-based cluster interpreter for yeast by Robinson (2002)
  4. 10.1093/bioinformatics/btg363 / Bioinformatics / Characterizing gene sets with FuncAssociate by Berriz (2003)
  5. 10.1093/bioinformatics/btg114 / Bioinformatics / GeneMerge—post-genomic analysis, data mining, and hypothesis testing by Castillo-Davis (2003)
  6. 10.1186/gb-2003-4-5-p3 / Genome Biol. / DAVID: Database for Annotation, Visualization, and Integrated Discovery by Dennis (2003)
  7. 10.1186/gb-2003-4-1-r7 / Genome Biol. / MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data by Doniger (2003)
  8. 10.1186/gb-2003-4-10-r70 / Genome Biol. / Identifying biological themes within lists of genes with EASE by Hosack (2003)
  9. 10.1093/bioinformatics/btg291 / Bioinformatics / GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data by Martinez-Cruz (2003)
  10. 10.1186/gb-2003-4-4-r28 / Genome Biol. / GoMiner: a resource for biological interpretation of genomic and proteomic data by Zeeberg (2003)
  11. 10.1016/j.tibtech.2005.05.011 / Trends Biotechnol. / Pathways to the analysis of microarray data by Curtis (2005)
  12. 10.1093/bioinformatics/bti565 / Bioinformatics / Ontological analysis of gene expression data: current tools, limitations, and open problems by Khatri (2005)
  13. 10.1093/bioinformatics/btg455 / Bioinformatics / FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes by Al-Shahrour (2004)
  14. 10.1093/bioinformatics/bth088 / Bioinformatics / GOstat: find statistically overrepresented Gene Ontologies within a group of genes by Beissbarth (2004)
  15. 10.1093/bioinformatics/bth456 / Bioinformatics / GO::TermFinder–open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes by Boyle (2004)
  16. 10.1186/1471-2105-5-34 / BMC Bioinformatics / Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments by Breitling (2004)
  17. 10.1186/1471-2105-5-193 / BMC Bioinformatics / Comparing functional annotation analyses with Catmap by Breslin (2004)
  18. 10.1186/gb-2004-5-12-r101 / Genome Biol. / GOToolBox: functional analysis of gene datasets based on Gene Ontology by Martin (2004)
  19. 10.1093/nar/gkh432 / Nucleic Acids Res. / GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining by Masseroli (2004)
  20. 10.1093/bioinformatics/bth295 / Bioinformatics / THEA: ontology-driven analysis of microarray data by Pasquier (2004)
  21. 10.1093/bioinformatics/bth056 / Bioinformatics / CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology by Shah (2004)
  22. 10.1093/bioinformatics/bth293 / Bioinformatics / GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms by Smid (2004)
  23. 10.1093/nar/gkh443 / Nucleic Acids Res. / GOAL: automated Gene Ontology analysis of expression profiles by Volinia (2004)
  24. 10.1186/1471-2105-5-16 / BMC Bioinformatics / GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies by Zhang (2004)
  25. 10.2165/00822942-200403040-00009 / Appl. Bioinformatics / GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space by Zhong (2004)
  26. 10.1093/nar/gki456 / Nucleic Acids Res. / BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments by Al-Shahrour (2005)
  27. {'key': 'key\n\t\t\t\t20170515031309_B27', 'first-page': '106', 'article-title': 'Biological profiling of gene groups utilizing Gene Ontology', 'volume': '16', 'author': 'Bluthgen', 'year': '2005', 'journal-title': 'Genome Inform.'} / Genome Inform. / Biological profiling of gene groups utilizing Gene Ontology by Bluthgen (2005)
  28. 10.1093/nar/gki484 / Nucleic Acids Res. / T-profiler: scoring the activity of predefined groups of genes using gene expression data by Boorsma (2005)
  29. 10.1186/1471-2105-6-144 / BMC Bioinformatics / PAGE: parametric analysis of gene set enrichment by Kim (2005)
  30. 10.1186/1471-2105-6-161 / BMC Bioinformatics / FACT–a framework for the functional interpretation of high-throughput experiments by Kokocinski (2005)
  31. 10.1186/1471-2105-6-269 / BMC Bioinformatics / ErmineJ: tool for functional analysis of gene expression data sets by Lee (2005)
  32. 10.1186/1471-2105-6-189 / BMC Bioinformatics / GObar: a gene ontology based analysis and visualization tool for gene sets by Lee (2005)
  33. 10.1093/bioinformatics/bti551 / Bioinformatics / BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks by Maere (2005)
  34. 10.1186/gb-2005-6-9-r81 / Genome Biol. / L2L: a simple tool for discovering the hidden significance in microarray expression data by Newman (2005)
  35. 10.1073/pnas.0506580102 / Proc. Natl Acad. Sci. USA / Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles by Subramanian (2005)
  36. 10.2144/05382RR04 / Biotechniques / MEGO: gene functional module expression based on gene ontology by Tu (2005)
  37. 10.1093/bioinformatics/bti574 / Bioinformatics / goCluster integrates statistical analysis and functional interpretation of microarray expression data by Wrobel (2005)
  38. 10.1093/bioinformatics/bth495 / Bioinformatics / OntologyTraverser: an R package for GO analysis by Young (2005)
  39. 10.1186/1471-2105-6-168 / BMC Bioinformatics / 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) by Zeeberg (2005)
  40. 10.1093/nar/gki475 / Nucleic Acids Res. / WebGestalt: an integrated system for exploring gene sets in various biological contexts by Zhang (2005)
  41. 10.1093/bioinformatics/btl140 / Bioinformatics / Improved scoring of functional groups from gene expression data by decorrelating GO graph structure by Alexa (2006)
  42. 10.1186/1471-2105-7-470 / BMC Bioinformatics / GeneTools—application for functional annotation and statistical hypothesis testing by Beisvag (2006)
  43. 10.1142/S0219720006002181 / J. Bioinform. Comput. Biol. / Clustering biological annotations and gene expression data to identify putatively co-regulated biological processes by Henegar (2006)
  44. 10.1186/1471-2105-7-426 / BMC Bioinformatics / Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data by Lewin (2006)
  45. 10.1093/bioinformatics/btl378 / Bioinformatics / ADGO: analysis of differentially expressed gene sets using composite GO annotation by Nam (2006)
  46. {'key': 'key\n\t\t\t\t20170515031309_B46', 'first-page': '108', 'article-title': 'Gene class expression: analysis tool of Gene Ontology terms with gene expression data', 'volume': '5', 'author': 'Pereira', 'year': '2006', 'journal-title': 'Genet. Mol. Res.'} / Genet. Mol. Res. / Gene class expression: analysis tool of Gene Ontology terms with gene expression data by Pereira (2006)
  47. 10.1093/bib/bbl013 / Brief Bioinform. / Circumventing the cut-off for enrichment analysis by Rubin (2006)
  48. 10.1093/nar/gkl329 / Nucleic Acids Res. / JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information by Scheer (2006)
  49. 10.1186/1471-2105-7-443 / BMC Bioinformatics / GOLEM: an interactive graph-based gene-ontology navigation and analysis tool by Sealfon (2006)
  50. 10.1186/1471-2105-7-S2-S23 / BMC Bioinformatics / GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology tool for analysis of genomic and proteomic data by Sun (2006)
  51. 10.1186/1471-2105-7-535 / BMC Bioinformatics / PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments by Usadel (2006)
  52. 10.1186/1471-2105-7-86 / BMC Bioinformatics / BayGO: Bayesian analysis of ontology term enrichment in microarray data by Vencio (2006)
  53. 10.1110/ps.062184006 / Protein Sci. / A categorization approach to automated ontological function annotation by Verspoor (2006)
  54. 10.1093/nar/gkl031 / Nucleic Acids Res. / WEGO: a web tool for plotting GO annotations by Ye (2006)
  55. 10.1186/1471-2105-8-114 / BMC Bioinformatics / From genes to functional classes in the study of biological systems by Al-Shahrour (2007)
  56. 10.1093/nar/gkm260 / Nucleic Acids Res. / FatiGO + : a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments by Al-Shahrour (2007)
  57. 10.1093/nar/gkm323 / Nucleic Acids Res. / GeneTrail—advanced gene set enrichment analysis by Backes (2007)
  58. 10.1093/bioinformatics/btl658 / Bioinformatics / FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes by Blom (2007)
  59. 10.1186/gb-2007-8-1-r3 / Genome Biol. / GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists by Carmona-Saez (2007)
  60. 10.1186/gb-2007-8-9-r183 / Genome Biol. / The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists by Huang da (2007)
  61. 10.1093/nar/gkm415 / Nucleic Acids Res. / DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists by Huang da (2007)
  62. 10.1093/nar/gkm327 / Nucleic Acids Res. / Onto-Tools: new additions and improvements in 2006 by Khatri (2007)
  63. 10.1093/bioinformatics/btm144 / Bioinformatics / GAzer: gene set analyzer by Kim (2007)
  64. 10.1093/nar/gkm226 / Nucleic Acids Res. / g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments by Reimand (2007)
  65. 10.1186/1471-2105-8-426 / BMC Bioinformatics / DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis by Sherman (2007)
  66. 10.1186/1471-2164-8-246 / BMC Genomics / EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species by Zhou (2007)
  67. 10.1093/nar/gkn251 / Nucleic Acids Res. / PaLS: filtering common literature, biological terms and pathway information by Alibes (2008)
  68. 10.1093/nar/gkn239 / Nucleic Acids Res. / ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data by Antonov (2008)
  69. 10.1093/bioinformatics/btn250 / Bioinformatics. / Ontologizer 2.0 - A multifunctional tool for GO term enrichment analysis and data exploration by Bauer (2008)
  70. 10.1093/nar/gkn276 / Nucleic Acids Res. / GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis by Zheng (2008)
  71. 10.1186/1471-2105-8-166 / BMC Bioinformatics / GOSim—an R-package for computation of information theoretic GO similarities between terms and gene products by Frohlich (2007)
  72. 10.1186/1471-2164-8-30 / BMC Genomics / GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology by Zhu (2007)
  73. 10.1186/1471-2105-8-383 / BMC Bioinformatics / ProbCD: enrichment analysis accounting for categorization uncertainty by Vencio (2007)
  74. 10.1093/nar/gkn256 / Nucleic Acids Res. / SerbGO: searching for the best GO tool by Mosquera (2008)
  75. 10.1038/nrg2363 / Nat. Rev. Genet. / Use and misuse of the gene ontology annotations by Rhee (2008)
  76. 10.1093/bioinformatics/btl633 / Bioinformatics / Enrichment or depletion of a GO category within a class of genes: which test? by Rivals (2007)
  77. 10.1186/gb-2007-8-5-r74 / Genome Biol. / Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies by Nilsson (2007)
  78. 10.1093/bioinformatics/btm558 / Bioinformatics / Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories by Yang (2008)
  79. 10.1093/bioinformatics/btl599 / Bioinformatics / Extensions to gene set enrichment by Jiang (2007)
  80. 10.1093/bioinformatics/btm051 / Bioinformatics / Analyzing gene expression data in terms of gene sets: methodological issues by Goeman (2007)
  81. 10.1093/bib/bbl019 / Brief Bioinform. / Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL by Gold (2007)
  82. 10.1038/nprot.2008.211 / Nat. Protoc. / Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources by Huang (2008)
  83. 10.1093/bioinformatics/bth921 / Bioinformatics / The gene ontology categorizer by Joslyn (2004)
  84. 10.1186/1471-2105-8-332 / BMC Bioinformatics / How to decide which are the most pertinent overly-represented features during gene set enrichment analysis by Barriot (2007)
  85. 10.1111/j.2517-6161.1995.tb02031.x / J. R. Stat. Soc. B / Controlling the false discovery rate: a practical and powerful approach to multiple testing by Benjamini (1995)
  86. 10.1214/ss/1056397487 / Stat. Sci. / Multiple hypothesis testing in microarray experiments by Dudoit (2003)
  87. 10.1093/bioinformatics/btl372 / Bioinformatics / Babel's tower revisited: a universal resource for cross-referencing across annotation databases by Draghici (2006)
  88. 10.1186/1471-2105-6-72 / BMC Bioinformatics / GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments by Kirov (2005)
  89. 10.1093/nar/gkl993 / Nucleic Acids Res. / Entrez Gene: gene-centered information at NCBI by Maglott (2007)
  90. 10.1093/nar/gkm895 / Nucleic Acids Res. / The universal protein resource (UniProt) by The UniProt Consortium (2008)
  91. 10.1093/nar/gkg040 / Nucleic Acids Res. / The protein information resource by Wu (2003)
  92. 10.1186/gb-2003-4-4-r27 / Genome Biol. / MatchMiner: a tool for batch navigation among gene and gene product identifiers by Bussey (2003)
  93. 10.1186/1471-2105-8-9 / BMC Bioinformatics / IDconverter and IDClight: conversion and annotation of gene and protein IDs by Alibes (2007)
Dates
Type When
Created 16 years, 9 months ago (Nov. 25, 2008, 10:58 p.m.)
Deposited 7 months ago (Feb. 4, 2025, 12:08 p.m.)
Indexed 12 hours, 30 minutes ago (Sept. 6, 2025, 4:13 p.m.)
Issued 16 years, 9 months ago (Nov. 25, 2008)
Published 16 years, 9 months ago (Nov. 25, 2008)
Published Online 16 years, 9 months ago (Nov. 25, 2008)
Published Print 16 years, 8 months ago (Jan. 1, 2009)
Funders 0

None

@article{Huang_2008, title={Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists}, volume={37}, ISSN={0305-1048}, url={http://dx.doi.org/10.1093/nar/gkn923}, DOI={10.1093/nar/gkn923}, number={1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Huang, Da Wei and Sherman, Brad T. and Lempicki, Richard A.}, year={2008}, month=nov, pages={1–13} }