FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes

Bioinformatics

Volumn 20, Issue 4, 2004, Pages 578-580

  Al Shahrour, Fátima ^a   Díaz Uriarte, Ramón ^a   Dopazo, Joaquín ^a  

^a Bioinformatics Unit   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BIOINFORMATICS; DNA MICROARRAY; EMBL NUCLEOTIDE SEQUENCE DATABASE; FATIGO; FLY; GENETIC ANALYSIS; GENETIC DATABASE; GENOME ANALYSIS; HUMAN; INFORMATION PROCESSING; INTERNET; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; STATISTICAL ANALYSIS; SWISS-PROT; WORM;

EID: 1542399989     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg455     Document Type: Article

References (17)

1. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene Ontology: Tool for the unification of biology. Nat. Genet., 25, 25-29.
2. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 289-300.
3. Benjamini,Y. and Yekutieli,D. (2001) The control of the false discovery rate in multiple testing under dependency. Ann. Stat., 29, 1165-1188.
4. Blaschke,C., Hirschman,L. and Valencia,A. (2002) Information extraction in molecular biology. Brief. Bioinform., 3, 154-165.
5. Doniger,S.W., Salomonis,N., Dahlquist,K.D., Vranizan,K., Lawlor,S.C. and Conklin,B.R. (2003) MAPPFinder: Using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol., 4, R7.
6. Dudoit,S., Shaffer,J.P. and Boldrick,J.C. (2002) Múltiple hypothesis testing in microarray experiments. Technical Report #110, Division of Biostatistics, UC Berkeley.
7. Herrero,J., Al-Shahrour,F., Díaz-Uriarte,R., Mateos,Á., Vaquerizas,J.M., Santoyo,J. and Dopazo,J. (2003) GEPAS, a web-based resource for microarray gene expression data analysis. Nucleic Acids Res., 31, 3461-3467.
8. Jenssen,T.-K., Laegreid,A., Komorowski,J. and Hovig,E. (2000) A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28, 21-28.
9. Khatri,P., Draghici,S., Ostermeier,G.C. and Krawetz,S.A. (2002) Profiling gene expression using onto-express. Genomics, 79, 1-5.
10. Mateos,A., Herrero,J., Tamames,J. and Dopazo,J. (2002) Supervised neural networks for clustering conditions in DNA array data after reducing noise by clustering gene expression profiles. In Lin,S. and Johnson,K. (eds), Methods of Microarray Data Analysis II. Kluwer Academic Publishers, Boston. pp. 91-103.
11. Oliveros,J.C., Blaschke,C., Herrero,J., Dopazo,J. and Valencia,A. (2000) Expression profiles and biological function. Genome Inform., 10, 106-117.
12. Pavlidis,P., Lewis,D.P. and Noble,W.S. (2002) Exploring gene expression data with class scores. Pac. Symp. Biocomput., 7, 474-485.
13. Raychaudhuri,S., Schutze,H. and Altman,R.B. (2002) Using text analysis to identify functionally coherent gene groups. Genome Res., 12, 1582-1590.
14. Reiner,A., Yekutieli,D. and Benjamini,Y. (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics, 19, 368-375.
15. Robinson,M.D., Grigull,J., Mohammad,N. and Hughes,T.R. (2002) FunSpect: A web-based cluster interpreter for yeast. BMC Bioinformatics, 3, 1-5.
16. Slonim,D.K. (2002) From patterns to pathways: Gene expression data analysis comes of age. Nat. Genet., 32, (suppl. The Chipping Forecast), 502-508.
17. Westfall,P.H. and Young,S.S. (1993) Resampling-Based Multiple Testing. John Wiley & Sons, New York.