Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes

Series on Advances in Bioinformatics and Computational Biology

Volumn 3, Issue , 2006, Pages 247-256

  Huang, Shao Shan ^a,b   Fulton, Debra L ^a,b   Arenillas, David J ^a,b   Perco, Paul ^c   Ho Sui, Shannan J ^a,b   Mortimer, James R ^d   Wasserman, Wyeth W ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c MEDICAL UNIVERSITY OF VIENNA   (Austria)

^d MERCK FROSST CENTRE FOR THERAPEUTIC RESEARCH   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS ALGORITHMS; ANALYSIS SYSTEM; BINDING PROPERTIES; COMBINATORIAL INTERACTIONS; COMBINATORIAL PROPERTIES; COMPUTATIONAL CHALLENGES; CROSS-SPECIES; FOOTPRINTING; FUNDAMENTAL PROBLEM; GENE EXPRESSION DATA; GENETIC INFORMATION; MOTIF MODEL; REFERENCE COLLECTIONS; SEQUENCE COMPARISONS; TRANSCRIPTION FACTOR BINDING SITES; TRANSCRIPTION REGULATIONS;

ALGORITHMS; BINDING ENERGY; BIOINFORMATICS; GENES; PLANTS (BOTANY); TRANSCRIPTION; TRANSCRIPTION FACTORS;

BINDING SITES;

EID: 84863012344     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (17)

1. M. I. Arnone and E. H. Davidson. The hardwiring of development: organization and function of genomic regulatory systems. Development, 124(10):1851-64, 1997. (Pubitemid 27270255)
2. N. Bluthgen, S. M. Kielbasa, and H. Herzel. Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res, 33(1):272-9, 2005. (Pubitemid 40276948)
3. S. J. Ho Sui, J. R. Mortimer, D. J. Arenillas, J. Brumm, C. J. Walsh, B. P. Kennedy, and W. W. Wasserman. oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res, 33(10):3154-64, 2005. (Pubitemid 41194459)
4. J. D. Hughes, P. W. Estep, S. Tavazoie, and G. M. Church. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol, 296(5):1205-14, 2000.
5. G. Kreiman. Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes. Nucleic Acids Res, 32(9):2889-900, 2004.
6. B. Lenhard, A. Sandelin, L. Mendoza, P. Engstrom, N. Jareborg, and W. W. Wasserman. Identification of conserved regulatory elements by comparative genome analysis. J Biol, 2(2):13, 2003.
7. C. S. Madsen, J. C. Hershey, M. B. Hautmann, S. L. White, and G. K. Owens. Expression of the smooth muscle myosin heavy chain gene is regulated by a negative-acting GC-rich element located between two positive-acting serum response factor-binding elements. J Biol Chem, 272(10):6332-40, 1997. (Pubitemid 27118108)
8. J. L. Moran, Y. Li, A. A. Hill, W. M. Mounts, and C. P. Miller. Gene expression changes during mouse skeletal myoblast differentiation revealed by transcriptional profiling. Physiol Genomics, 10(2):103-11, 2002. (Pubitemid 135707434)
9. S. Nelander, P. Mostad, and P. Lindahl. Prediction of cell type-specific gene modules: identification and initial characterization of a core set of smooth muscle-specific genes. Genome Res, 13(8):1838-54, 2003. (Pubitemid 36987190)
10. A. Sandelin, W. Alkema, P. Engstrom, W. W. Wasserman, and B. Lenhard. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res, 32(Database issue):D91-4, 2004. (Pubitemid 38081611)
11. A. Sandelin, A. Hoglund, B. Lenhard, and W. W. Wasserman. Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct Integr Genomics, 3(3):125-34, 2003. (Pubitemid 40796211)
12. R. Sharan, A. Ben-Hur, G. G. Loots, and I. Ovcharenko. CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Res, 32(Web Server issue):W253-6, 2004. (Pubitemid 38997339)
13. P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, and B. Futcher. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell, 9(12):3273-97, 1998. (Pubitemid 28551928)
14. K. K. Tomczak, V. D. Marinescu, M. F. Ramoni, D. Sanoudou, F. Montanaro, M. Han, L. M. Kunkel, I. S. Kohane, and A. H. Beggs. Expression profiling and identification of novel genes involved in myogenic differentiation. FASEB J, 18(2):403-5, 2004.
15. W. W. Wasserman and J. W. Fickett. Identification of regulatory regions which confer musclespecific gene expression. J Mol Biol, 278(1):167-81, 1998. (Pubitemid 28196158)
16. W. W. Wasserman and A. Sandelin. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet, 5(4):276-87, 2004. (Pubitemid 38435623)
17. R. Yamashita, Y. Suzuki, S. Sugano, and K. Nakai. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene, 350(2):129-36, 2005. (Pubitemid 40719057)