Identifying biological themes within lists of genes with EASE

Genome Biology

Volumn 4, Issue 10, 2003, Pages

  Hosack, Douglas A ^a   Dennis, Glynn ^a   Sherman, Brad T ^a   Lane, H Clifford ^b   Lempicki, Richard A ^a  

^a SAIC FREDERICK INC   (United States)

^b NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

Biological Theme; Expression Analysis Systematic Explorer; Gene List; Online Tool; Theme Discovery

Indexed keywords

ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DRUG ANALYSIS; FUNCTIONAL GENOMICS; GENE; HUMAN; PROTEOMICS; BIOLOGY; COMPUTER PROGRAM; DNA MICROARRAY; GENETIC DATABASE; GENOMICS; INTERNET; METHODOLOGY; PHYSIOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENES; GENOMICS; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOMICS; SOFTWARE;

EID: 0344319833     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2003-4-10-r70     Document Type: Article

References (36)

1. Heller MJ: DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng. 2002, 4: 129-153. 10.1146/annurev.bioeng.4.020702.153438. DOI: 10.1146/annurev.bioeng.4.020702.153438
2. Quackenbush J: Microarray data normalization and transformation. Nat Genet. 2002, 32 Suppl: 496-501. 10.1038/ng1032. DOI: 10.1038/ng1032
3. Slonim DK: From patterns to pathways: gene expression data analysis comes of age. Nat Genet. 2002, 32 Suppl: 502-508. 10.1038/ng1033. DOI: 10.1038/ng1033
4. Pruitt KD, Katz KS, Sicotte H, Maglott DR: Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet. 2000, 16: 44-47. 10.1016/S0168-9525(99)01882-X. DOI: 10.1016/S0168-9525(99)01882-X
5. The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genet. 2000, 25: 25-29. 10.1038/75556. DOI: 10.1038/75556
6. Bairoch A, Boeckmann B: The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 1991, 19 Suppl: 2247-2249. DOI: 10.1093/nar/19.suppl.2247
7. Wu CH, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu Z, Ledley RS, Lewis KC, Mewes H, Orcutt BC, et al: The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res. 2002, 30: 35-37. 10.1093/nar/30.1.35. DOI: 10.1093/nar/30.1.35
8. Fleiss JL: Statistical Methods for Rates and Proportions. 1981, New York: John Wiley
9. Tukey JW: Bias and confidence in not quite large samples. Ann Math Stat. 1958, 29: 614- DOI: 10.1214/aoms/1177706647
10. The FlyBase Consortium: The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 2003, 31: 172-175. 10.1093/nar/gkg094. DOI: 10.1093/nar/gkg094
11. Blake JA, Richardson JE, Bult CJ, Kadin JA, Eppig JT, Mouse Genome Database Group: MGD: The Mouse Genome Database. Nucleic Acids Res. 2003, 31: 193-195. 10.1093/nar/gkg047. DOI: 10.1093/nar/gkg047
12. Rat Genome Database. [http://rgd.mcw.edu/]
13. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, et al: Database resources of the National Center for Biotechnology. Nucleic Acids Res. 2003, 31: 28-33. 10.1093/nar/gkg033. DOI: 10.1093/nar/gkg033
14. Affymetrix, Inc. [http://www.affymetrix.com]
15. Kanehisa M, Goto S, Kawashima S, Nakaya A: The KEGG databases at GenomeNet. Nucleic Acids Res. 2002, 30: 42-46. 10.1093/nar/30.1.42. DOI: 10.1093/nar/30.1.42
16. Becker KG, White SL, Muller J, Engel J: BBID: the biological biochemical image database. Bioinformatics. 2000, 16: 745-746. 10.1093/bioinformatics/16.8.745. DOI: 10.1093/bioinformatics/16.8.745
17. Proteome HumanPSD database. [http://www.incyte.com/documents/HumanPSD_Brochure.pdf]
18. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res. 2002, 30: 276-280. 10.1093/nar/30.1.276. DOI: 10.1093/nar/30.1.276
19. Schultz J, Milpetz F, Bork P, Ponting CP: SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA. 1998, 95: 5857-5864. 10.1073/pnas.95.11.5857. DOI: 10.1073/pnas.95.11.5857
20. Microsoft, Inc. [http://www.microsoft.com/office/excel/default.asp]
21. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA: DAVID: Database for Annotation, Visualization and Integrated Discovery. Genome Biol. 2003, 4: P3-10.1186/gb-2003-4-5-p3. DOI: 10.1186/gb-2003-4-5-p3
22. Cui X, Churchill GA: Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 2003, 4: 210-10.1186/gb-2003-4-4-210. DOI: 10.1186/gb-2003-4-4-210
23. Efron B: Bootstrap methods: another look at the jackknife. Ann Statistics. 1979, 7: 1-26. DOI: 10.1214/aos/1176344552
24. Kayo T, Allison DB, Weindruch R, Prolla TA: Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys. Proc Natl Acad Sci USA. 2001, 98: 5093-5098. 10.1073/pnas.081061898. DOI: 10.1073/pnas.081061898
25. Wu CC, MacCoss MJ, Howell KE, Yates JR: A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol. 2003, 21: 532-538. 10.1038/nbt819. DOI: 10.1038/nbt819
26. Gnatenko DV, Dunn JJ, McCorkle SR, Weissmann D, Perrotta PL, Bahou WF: Transcript profiling of human platelets using microarray and serial analysis of gene expression. Blood. 2003, 101: 2285-2293. 10.1182/blood-2002-09-2797. DOI: 10.1182/blood-2002-09-2797
27. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc Natl Acad Sci USA. 2001, 98: 31-36. 10.1073/pnas.011404098. DOI: 10.1073/pnas.98.1.31
28. Sidorov IA, Hosack DA, Gee D, Yang J, Cam MC, Lempicki RA, Dimitrov DS: Oligonucleotide microarray data distribution and normalization. Inform Sci. 2002, 146: 65-71.
29. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 2001, 98: 5116-5121. 10.1073/pnas.091062498. DOI: 10.1073/pnas.091062498
30. Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, Conklin BR: MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 2003, 4: R7-10.1186/gb-2003-4-1-r7. DOI: 10.1186/gb-2003-4-1-r7
31. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, et al: GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 2003, 4: R28-10.1186/gb-2003-4-4-r28. DOI: 10.1186/gb-2003-4-4-r28
32. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR: GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet. 2002, 31: 19-20. 10.1038/ng0502-19. DOI: 10.1038/ng0502-19
33. Cicala C, Arthos J, Selig SM, Dennis G, Hosack DA, Van Ryk D, Spangler ML, Steenbeke TD, Khazanie P, Gupta N, et al: HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc Natl Acad Sci USA. 2002, 99: 9380-9385. 10.1073/pnas.142287999. DOI: 10.1073/pnas.142287999
34. Chun TW, Justement JS, Lempicki RA, Yang J, Dennis G, Hallahan CW, Sanford C, Pandya P, Liu S, McLaughlin M, et al: Gene expression and viral production in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc Natl Acad Sci USA. 2003, 100: 1908-1913. 10.1073/pnas.0437640100. DOI: 10.1073/pnas.0437640100
35. DAVID: download EASE. [http://david.niaid.nih.gov/david/ease.htm]
36. DAVID: Database for Annotation, Visualization, and Integrated Discovery. [http://david.niaid.nih.gov]