FUNC: A package for detecting significant associations between gene sets and ontological annotations

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Prüfer, Kay ^a   Muetzel, Bjoern ^a   Do, Hong Hai ^b   Weiss, Gunter ^a   Khaitovich, Philipp ^a,c   Rahm, Erhard ^b   Pääbo, Svante ^a   Lachmann, Michael ^a   Enard, Wolfgang ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ERROR RATE; EXPERIMENTAL METHODS; FALSE DISCOVERY RATE; GENE ONTOLOGY; GENE SETS; GENOME-WIDE SEQUENCES; PROGRAM PACKAGES; STATISTICAL SIGNIFICANCE;

ONTOLOGY; SOFTWARE PACKAGES; WEB SERVICES;

GENE EXPRESSION;

ALGORITHM; ANALYTICAL ERROR; ARTICLE; BINOMIAL DISTRIBUTION; COMPARATIVE GENE MAPPING; COMPUTER PROGRAM; CONTINGENCY TABLE; CONTROLLED STUDY; FALSE POSITIVE RESULT; GENE EXPRESSION; GENETIC ASSOCIATION; GEOMETRY; HUMAN; INTERNET; MOLECULAR GENETICS; NONHUMAN; NULL HYPOTHESIS; RANK SUM TEST; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; STATISTICAL SIGNIFICANCE; ANIMAL; AUTOMATED PATTERN RECOGNITION; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENOME; INFORMATION RETRIEVAL; MOLECULAR EVOLUTION; PROCEDURES; STATISTICAL ANALYSIS;

ALGORITHMS; ANIMALS; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENOME; HUMANS; INFORMATION STORAGE AND RETRIEVAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 33847173733     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-41     Document Type: Article

References (36)

1. The_Gene_Ontology_Consortium Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000 25 1 25-29 10.1038/ 75556 10802651
2. Draghici S Khatri P Martins RP Ostermeier GC Krawetz SA Global functional profiling of gene expression Genomics 2003 81 2 98-104 10.1016/S0888-7543(02)00021-6 12620386
3. Young A Whitehouse N Cho J Shaw C OntologyTraverser: An R package for GO analysis Bioinformatics 2005 21 2 275-276 10.1093/bioinformatics/bth495 15333457
4. Pandey R Guru RK Mount DW Pathway Miner: Extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data Bioinformatics 2004 20 13 2156-2158 10.1093/bioinformatics/bth215 15145817
5. Beissbarth T Speed TP GOstat: Find statistically overrepresented Gene Ontologies within a group of genes Bioinformatics 2004 20 9 1464-1465 10.1093/bioinformatics/bth088 14962934
6. Masseroli M Martucci D Pinciroli F GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining Nucleic Acids Res 2004 32 Web Server issue W293-300 441570 15215397
7. Zhang B Schmoyer D Kirov S Snoddy J GOTree Machine (GOTM): A web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies BMC Bioinformatics 2004 5 16 373441 14975175 10.1186/ 1471-2105-5-16
8. Ben-Shaul Y Bergman H Soreq H Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression Bioinformatics 2005 21 7 1129-1137 10.1093/bioinformatics/bti149 15550480
9. Al-Shahrour F Diaz-Uriarte R Dopazo J FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes Bioinformatics 2004 20 4 578-580 10.1093/bioinformatics/btg455 14990455
10. Berriz GF King OD Bryant B Sander C Roth FP Characterizing gene sets with FuncAssociate Bioinformatics 2003 19 18 2502-2504 10.1093/ bioinformatics/btg363 14668247
11. Castillo-Davis CI Hartl DL GeneMerge--post-genomic analysis, data mining, and hypothesis testing Bioinformatics 2003 19 7 891-892 10.1093/ bioinformatics/btg114 12724301
12. Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and powerful approach to multiple testing J R Statist Soc B 1995 57 1 289-300
13. Manly KF Nettleton D Hwang JT Genomics, prior probability, and statistical tests of multiple hypotheses Genome Res 2004 14 6 997-1001 10.1101/gr.2156804 15173107
14. Reiner A Yekutieli D Benjamini Y Identifying differentially expressed genes using false discovery rate controlling procedures Bioinformatics 2003 19 3 368-375 10.1093/bioinformatics/btf877 12584122
15. Ge YC Dudoit S Speed TP Resampling-based multiple testing for microarray data analysis Test 2003 12 1 1-77
16. Barry WT Nobel AB Wright FA Significance analysis of functional categories in gene expression studies: A structured permutation approach Bioinformatics 2005 21 9 1943-1949 10.1093/bioinformatics/bti260 15647293
17. Mootha VK Lindgren CM Eriksson KF Subramanian A Sihag S Lehar J Puigserver P Carlsson E Ridderstrale M Laurila E Houstis N Daly MJ Patterson N Mesirov JP Golub TR Tamayo P Spiegelman B Lander ES Hirschhorn JN Altshuler D Groop LC PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes Nat Genet 2003 34 3 267-273 10.1038/ng1180 12808457
18. Volinia S Evangelisti R Francioso F Arcelli D Carella M Gasparini P GOAL: Automated Gene Ontology analysis of expression profiles Nucleic Acids Res 2004 32 Web Server issue W492-9 441581 15215435
19. Zeeberg BR Qin H Narasimhan S Sunshine M Cao H Kane DW Reimers M Stephens R Bryant D Burt SK Elnekave E Hari DM Wynn TA Cunningham-Rundles C Stewart DM Nelson D Weinstein JN 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 2005 6 1 168 1190154 15998470 10.1186/1471-2105-6-168
20. Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich AP Pomeroy SL Golub TR Lander ES Mesirov J Gene set enrichment analysis: A knowledge based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci U S A 2005 102 43 15545-15550 1239896 16199517 10.1073/pnas.0506580102
21. Tian L Greenberg SA Kong SW Altschuler J Kohane IS Park PJ Discovering statistically significant pathways in expression profiling studies Proc Natl Acad Sci U S A 2005 102 38 13544 -3549 1200092 16174746 10.1073/ pnas.0506577102
22. Osier MV Zhao H Cheung KH Handling multiple testing while interpreting microarrays with the Gene Ontology Database BMC Bioinformatics 2004 5 124 518975 15350198 10.1186/1471-2105-5-124
23. Breslin T Eden P Krogh M Comparing functional annotation analyses with Catmap BMC Bioinformatics 2004 5 1 193 543458 15588298 10.1186/ 1471-2105-5-193
24. McDonald JH Kreitman M Adaptive protein evolution at the Adh locus in Drosophila Nature 1991 351 6328 652-654 10.1038/351652a0 1904993
25. The_Chimpanzee_Sequencing∠d_Analysis_Consortium Initial sequence of the chimpanzee genome and comparison with the human genome Nature 2005 437 7055 69-87 10.1038/nature04072 16136131
26. Kelso J Visagie J Theiler G Christoffels A Bardien S Smedley D Otgaar D Greyling G Jongeneel CV McCarthy MI Hide T Hide W eVOC: A controlled vocabulary for unifying gene expression data Genome Res 2003 13 6A 1222-1230 403650 12799354 10.1101/gr.985203
27. Yekutieli D Benjamini Y Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics J STAT PLAN INFER 1999 82 1-2 171-196 10.1016/S0378-3758(99)00041-5
28. Westfall PH Young SS Resampling-Based Multiple Testing: Examples and Methods for p-value Adjustment New York, John Wiley & Sons, Inc. 1993
29. Velculescu VE Zhang L Vogelstein B Kinzler KW Serial analysis of gene expression Science 1995 270 5235 484-487 10.1126/science.270.5235.484 7570003
30. Fay JC Wu CI Sequence divergence, functional constraint, and selection in protein evolution Annu Rev Genomics Hum Genet 2003 4 213-235 10.1146/ annurev.genom.4.020303.162528 14527302
31. Damian D Gorfine M Statistical concerns about the GSEA procedure Nat Genet 2004 36 7 663; author reply 663 10.1038/ng0704-663a 15226741
32. Hsueh H Chen JJ Kodell RL Comparison of methods for estimating the number of true null hypotheses in multplicity testing J Biopharm Stat 2003 13 4 675-689 10.1081/BIP-120024202 14584715
33. Benjamini Y Yekutieli D The control of the false discovery rate in multiple testing under dependency Ann Stat 2001 29 1165-1188 10.1214/aos/ 1013699998
34. Alexa A Rahnenfuhrer J Lengauer T Improved scoring of functional groups from gene expression data by decorrelating GO graph structure Bioinformatics 2006 22 13 1600-1607 10.1093/bioinformatics/btl140 16606683
35. Gilad Y Man O Paabo S Lancet D Human specific loss of olfactory receptor genes Proc Natl Acad Sci U S A 2003 100 6 3324-3327 152291 12612342 10.1073/pnas.0535697100
36. Zeeberg BR Feng W Wang G Wang MD Fojo AT Sunshine M Narasimhan S Kane DW Reinhold WC Lababidi S Bussey KJ Riss J Barrett JC Weinstein JN GoMiner: a resource for biological interpretation of genomic and proteomic data Genome Biol 2003 4 4 R28 154579 12702209 10.1186/gb-2003-4-4-r28