STOP: Searching for transcription factor motifs using gene expression

Bioinformatics

Volumn 23, Issue 14, 2007, Pages 1737-1743

  Hertzberg, Libi ^a,b   Izraeli, Shai ^a   Domany, Eytan ^b  

^a TEL AVIV UNIVERSITY   (Israel)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; BIOINFORMATICS; DATA ANALYSIS SOFTWARE; DNA SEQUENCE; GENE EXPRESSION; GENE SEQUENCE; GENE TARGETING; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; INTERMETHOD COMPARISON; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS;

EID: 34547866080     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm249     Document Type: Article

References (14)

1. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Statist. Soc., 57, 289-300.
2. Boyer,L.A. et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell, 122, 947-956.
3. Chiang,D.Y. et al. (2001) Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics, 17, S49-S55.
4. Elkon,R. et al. (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res., 13, 773-780.
5. Hertzberg,L. et al. (2005) Finding motifs in promoter regions. J. Comput. Biol., 12, 314-330.
6. Kel,A.E. et al. (2003) MATCH: A tool for watching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31 3576-3579.
7. Kel,A. et al. (2006) Beyond microarrays: Finding key transcription factors controlling signal transduction pathways. BMC Bioinformatics 7 (Suppl. 2), S13.
8. Matys,V. et al. (2003) TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
9. Odom,D.T. et al. (2006) Core transcriptional regulatory circuitry in human hepatocytes. Mol. Sys. Biol., 2, 2006.0017 2006.0017 doi:10.1038/msb4100059 (see http://www.nature.com/msb/journal/ v2/n1/full/msb4100059.html).
10. Quandt,K. et al. (1905) MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
11. Rao,A. et al. (1997) Transcription factors of the NFAT family: regulation and Function. Ann. Rev. Immunol., 15, 707-747.
12. Ross,M.E. et al. (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood, 102 2951-2959.
13. Su,A.I. et al. (2004) A gene atlas of flie mouse and human protein-encoding transcriptomes. PNAS, 101, 6062-6067.
14. Tsafrir,D. et al. (2006) Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Res., 66 2129-2137.