RSIR: Regularized sliced inverse regression for motif discovery

Bioinformatics

Volumn 21, Issue 22, 2005, Pages 4169-4175

  Zhong, Wenxuan ^a   Zeng, Peng ^b   Ma, Ping ^c   Liu, Jun S ^a   Zhu, Yu ^d  

^a HARVARD UNIVERSITY   (United States)

^b AUBURN UNIVERSITY   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ANALYTICAL ERROR; ARTICLE; BIOINFORMATICS; CELL CYCLE; CONTROLLED STUDY; DNA MICROARRAY; FUNGAL GENETICS; GENE EXPRESSION; INTERMETHOD COMPARISON; NONHUMAN; PERFORMANCE; PRIORITY JOURNAL; PROTEIN MOTIF; REGRESSION ANALYSIS; SIMULATION; STATISTICAL MODEL; YEAST;

EID: 27944453151     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti680     Document Type: Article

References (25)

1. Beer,M.A. and Tavazoie,S. (2004) Predicting gene expression from sequence. Cell, 117, 185-198.
2. Bussemaker,H.J. et al. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171.
3. Castillo-Davis,C. and Hartl,D. (2003) Genemerge: Post-genomic analysis, data-mining and hypothesis. Bioinformatics, 19, 891-892.
4. Conlon,E. et al. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci. USA, 100, 3339-3344.
5. Cook,R.D. (1998) Regression Graphics: Ideas for Studying Regressions Through Graphics. John Wiley & Sons, New York.
6. Das,D. et al. (2004) Interacting models of cooperative gene regulation. Proc. Natl Acad. Sci. USA, 101, 16234-16239.
7. Gasch,A. et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
8. Harbison,C. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
9. Hastie,T. et al. (1995) Penalized discriminant analysis. Ann. Stat., 23, 73-102.
10. Jensen,S. et al. (2004) Computational discovery of gene regulatory binding motifs: A bayesian perspective. Stat. Sci., 19, 188-204.
11. Keles,S. et al. (2002) Identification of regulatory elements using a feature selection method. Bioinformatics, 18, 1167-1175.
12. Keles,S. et al. (2004) Regulatory motif finding using logic regression. Bioinformatics, 20, 2799-2811.
13. Lee,T. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
14. Li,K.C. (1991) Sliced inverse regression for dimension reduction. J. Am. Stat. Assoc., 86, 316-327.
15. Lieb,J.D. et al. (2001) Promoter-specific binding of rap1 revealed by genome-wise maps of protein-DNA association. Nat. Genet., 28, 327-334.
16. Liu,X. et al. (2002) An algorithm for finding protein-DNA interaction sites with applications to chromatin immunoprecipitation microarray experiments. Nat. Biotechnol., 27, 835-839.
17. Makhnevych,T. et al. (2003) Cell cycle regulated transport controlled by alterations in the nuclear pore complex. Cell, 115, 813-823.
18. Morrow,B.E. et al. (1993) A bipartite DNA-binding domain in yeast reb1p. Mol. Cell Biol., 13, 1173-1182.
19. Ren,B. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
20. Simon,I. et al. (2001) Serial regulation of transcriptionaj regulators in the yeast cell cycle. Cell, 106, 697-708.
21. Sinisi,S.E. and van der Laan,M.J. (2004) Deletion/substitution/addition algorithm in learning with applications in genomics. Stat. Appl. Genet. Mol. Biol., 3, 2799-2811.
22. 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.
23. Storey,J.D. (2002) A direct approach to false discovery rates. J. R. Stat. Soc. Ser. B, 64, 479-498.
24. Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
25. Yu,B. et al. (1999) Penalized discriminant analysis of in situ hyperspectral data for conifer species recognition. IEEE Trans. Geosci. Remote Sensing, 37, 2569-2577.