Study of coordinative gene expression at the biological process level

Bioinformatics

Volumn 21, Issue 18, 2005, Pages 3651-3657

  Yu, Tianwei ^a   Sun, Wei ^a   Yuan, Shinsheng ^a   Li, Ker Chau ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CELL ACTIVITY; CELL CYCLE; CONTROLLED STUDY; CORRELATION ANALYSIS; FOLLOW UP; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN MICROARRAY; SACCHAROMYCES CEREVISIAE; STRESS;

SACCHAROMYCES CEREVISIAE;

EID: 24644464205     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti599     Document Type: Article

References (28)

1. Alberts,B., Johnson,A., Lewis,J., Raff,M., Roberts,T. and Walter,P. (2002) Mol. Biol. Cell, 4th edn. Garland Publishing, NY.
2. Ashburner,M. et al. (2000) Gene Ontology: Tool for the unification of biology. Nat. Genet., 25, 25-29.
3. Benjamini,Y. and Yekutieli,D. (2001) The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29 1165-1188.
4. Berriz,G.F. et al. (2003) Characterizing gene sets with FuncAssociate. Bioinformatics, 19, 2502-2504.
5. Cheng,J. et al. (2004) NetAffx Gene Ontology Mining Tool: A visual approach for microarray data analysis. Bioinformatics, 20, 1462-1463.
6. Conlon,E.M. et al. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci. USA, 100, 3339-3344.
7. Draghici,S. et al. (2003) Global functional profiling of gene expression. Genomics, 81, 98-104.
8. Dwight,S.S. et al. (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res., 30, 69-72.
9. Eisen,M.B. et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95 14863-14868.
10. Gasch,A.P. et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 11, 4241-4257.
11. Giot,L. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
12. Ihmels,J. et al. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet., 31, 370-377.
13. Li,K.C. (2002) Genome-wide coexpression dynamics: Theory and application. Proc. Natl Acad. Sci. USA, 99, 16875-16880.
14. Li,K.C. et al. (2004) A system for enhancing genome-wide coexpression dynamics study. Proc. Natl Acad. Sci. USA, 101, 15561-15566.
15. Lord,P.W. et al. (2003) Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation. Bioinformatics, 19, 1275-1283.
16. Mootha,V.K. et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34, 267-273.
17. Palmgren,S. et al. (2002) Twinfilin, a molecular mailman for actin monomers. J. Cell Sci., 115, 881-886.
18. Pavlidis,P. et al. (2004) Using the gene ontology for microarray data mining: A comparison of methods and application to age effects in human prefrontal cortex. Neurochem. Res., 29, 1213-1222.
19. Qian,J. et al. (2003) Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics, 19, 1917-1926.
20. Qin,Z.S. et al. (2003) Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat. Biotechnol., 21, 435-439.
21. Reiner,A. et al. (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics, 19, 368-375.
22. Robinson,M.D. et al. (2002) FunSpec: A web-based cluster interpreter for yeast. BMC Bioinformatics, 3, 35.
23. Shannon,P. et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504.
24. Smid,M. and Dorssers,L.C. (2004) GO-Mapper: Functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics, 20, 2618-2625.
25. Spellman,P.T. et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
26. Tong,A.H. et al. (2003) Global mapping of the yeast genetic interaction network. Science, 303, 808-813.
27. Volinia,S. et al. (2004) GOAL: Automated Gene Ontology analysis of expression profiles. Nucleic Acids Res., 32, 492-499.
28. Zhou,X. et al. (2002) Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl Acad. Sci. USA, 99, 12783-12788.