TREMOR - A tool for retrieving transcriptional modules by incorporating motif covariance

Nucleic Acids Research

Volumn 35, Issue 21, 2007, Pages 7360-7371

  Singh, Larry N ^a   Wang, Li San ^a   Hannenhalli, Sridhar ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEPATOCYTE NUCLEAR FACTOR 1; HEPATOCYTE NUCLEAR FACTOR 3; HEPATOCYTE NUCLEAR FACTOR 4; MYOD PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SP1; TRANSCRIPTIONAL MODULE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CELL CYCLE; COMPUTER PROGRAM; CORRELATION ANALYSIS; COVARIANCE; DNA BINDING; DNA SEQUENCE; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; LIVER CELL; MUSCLE CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; STATISTICAL ANALYSIS; VALIDITY;

BINDING SITES; COMPUTER SIMULATION; GENES, CDC; HUMANS; LIVER; MUSCLES; PROMOTER REGIONS (GENETICS); SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 37549008295     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm885     Document Type: Article

References (59)

1. Kadonaga,J.T. (2004) Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell, 116, 247-257.
2. Ptashne,M. and Gann,A. (1997) Transcriptional activation by recruitment. Nature, 386, 569-577.
3. Segal,E. and Sharan,R., (2004) Proceedings of the Eigth Annual International Conference on Computational Molecular Biology, San Diego, CA. ACM Press, New York, USA, pp. 141-149.
4. Blanchette,M., Bataille,A.R., Chen,X., Poitras,C., Laganiere,J., Lefebvre,C., Deblois,G., Giguere,V., Ferretti,V. et al. (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 16, 656-668.
5. Sinha,S., Van Nimwegen,E. and Siggia,E.D. (2003) A probabilistic method to detect regulatory modules. Bioinformatics, 19(Suppl. 1), 1292-1301.
6. Zhao,G., Schriefer,L.A. and Stormo,G.D. (2007) Identification of muscle-specific regulatory modules in Caenorhabditis elegans. Genome Res., 17, 348-357.
7. Hannenhalli,S. and Levy,S. (2003) Transcriptional regulation of protein complexes and biological pathways. Mamm. Genome, 14, 611-619.
8. Matys,V., Kel-Margoulis,O.V., Fricke,E., Liebich,I., Land,S., Barre-Dirrie,A., Reuter,I., Chekmenev,D., Krull,M. et al. (2006) TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
9. Sandelin,A., Alkema,W., Engstrom,P., Wasserman,W.W. and Lenhard,B. (2004) JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91-D94.
10. Aerts,S., Thijs,G., Coessens,B., Staes,M., Moreau,Y. and De Moor,B. (2003) Toucan: Deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res., 31, 1753-1764.
11. Karanam,S. and Moreno,C.S. (2004) CONFAC: Automated application of comparative genomic promoter analysis to DNA microarray datasets. Nucleic Acids Res., 32, W475-W484.
12. Ho Sui,S.J., Mortimer,J.R., Arenillas,D.J., Brumm,J., Walsh,C.J., Kennedy,B.P. and Wasserman,W.W. (2005) oPOSSUM: Identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res., 33, 3154-3164.
13. Huang,S.S., Fulton,D.L., Arenillas,D.J., Perco,P., Ho Sui,S.J., Mortimer,J.R. and Wasserman,W.W. (2006) Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes. Adv. Bioinform. Comput. Biol., 3 3247.
14. Sharan,R., Ben-Hur,A., Loots,G.G. and Ovcharenko,I. (2004) CREME: cis-regulatory module explorer for the human genome. Nucleic Acids Res., 32, W253-W256.
15. Sandelin,A. and Wasserman,W.W. (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol., 338, 207-215.
16. Hannenhalli,S. and Wang,L.S. (2005) Enhanced position weight matrices using mixture models. Bioinformatics, 21(Suppl. 1), i204-i212.
17. Mahalanobis,P. (1936) On the generalized distance in statistics. Proc. Natl Inst. Sci. India, 2, 49-55.
18. Mahony,S., Auron,P.E. and Benos,P.V. (2007) DNA familial binding profiles made easy: Comparison of various motif alignment and clustering strategies. PLoS Comput. Biol., 3, e61.
19. Pilpel,Y., Sudarsanam,P. and Church,G.M. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29, 153-159.
20. Banerjee,N. and Zhang,M.Q. (2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res., 31, 7024-7031.
21. Cho,R.J., Huang,M., Campbell,M.J., Dong,H., Steinmetz,L., Sapinoso,L., Hampton,G., Elledge,S.J., Davis,R.W. et al. (2001) Transcriptional regulation and function during the human cell cycle. Nat. Genet., 27, 48-54.
22. Su,A.I., Wiltshire,T., Batalov,S., Lapp,H., Ching,K.A., Block,D., Zhang,J., Soden,R., Hayakawa,M. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067.
23. Storey,J.D. and Tibshirani,R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
24. Sharan,R., Ovcharenko,I., Ben-Hur,A. and Karp,R.M. (2003) CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics, 19(Suppl. 1), i283-i291.
25. Whitfield,M.L., Sherlock,G., Saldanha,A.J., Murray,J.I., Ball,C.A., Alexander,K.E., Matese,J.C., Perou,C.M., Hurt,M.M. et al. (2002) Identification of genes periodically expressed in the human cell cycle, & their expression in tumors. Mol. Biol. Cell, 13, 1977-2000.
26. Elkon,R., Linhart,C., Sharan,R., Shamir,R. and Shiloh,Y. (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res., 13, 773-780.
27. Ktistaki,E. and Talianidis,I. (1997) Modulation of hepatic gene expression by hepatocyte nuclear factor 1. Science, 277, 109-112.
28. Krivan,W. and Wasserman,W.W. (2001) A predictive model for regulatory sequences directing liver-specific transcription. Genome Res., 11, 1559-1566.
29. Wasserman,W.W. and Fickett,J.W. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278, 167-181.
30. Wasserman,W.W., Palumbo,M., Thompson,W., Fickett,J.W. and Lawrence,C.E. (2000) Human-mouse genome comparisons to locate regulatory sites. Nat. Genet., 26, 225-228.
31. Emberly,E., Rajewsky,N. and Siggia,E.D. (2003) Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics, 4, 57.
32. Nobrega,M.A., Zhu,Y., Plajzer-Frick,I., Afzal,V. and Rubin,E.M. (2004) Megabase deletions of gene deserts result in viable mice. Nature, 431, 988-993.
33. Birney,E., Stamatoyannopoulos,J.A., Dutta,A., Guigo,R., Gingeras,T.R., Margulies,E.H., Weng,Z., Snyder,M., Dermitzakis,E.T. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816.
34. Yao,M.W., Lim,H., Schust,D.J., Choe,S.E., Farago,A., Ding,Y., Michaud,S., Church,G.M. and Maas,R.L. (2003) Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the preimplantation uterus. Mol. Endocrinol., 17, 610-627.
35. Shukla,S. and Gupta,S. (2007) Apigenin-induced cell cycle arrest is mediated by modulation of MAPK, P13K-Akt, and loss of cyclin D1 associated retinoblastoma dephosphorylation in human prostate cancer cells. Cell Cycle, 6, 1102-1114.
36. Hale,T.K. and Braithwaite,A.W. (1999) The adenovirus oncoprotein E1a stimulates binding of transcription factor ETF to transcriptionally activate the p53 gene. J. Biol. Chem., 274, 23777-23786.
37. Yuan,X., Li,T., Wang,H., Zhang,T., Barua,M., Borgesi,R.A., Bubley,G.J., Lu,M.L. and Balk,S.P. (2006) Androgen receptor remains critical for cell-cycle progression in androgen-independent CWR22 prostate cancer cells. Am. J. Pathol., 169, 682-696.
38. McPherson,L.A., Loktev,A.V. and Weigel,R.J. (2002) Tumor suppressor activity of AP2alpha mediated through a direct interaction with p53. J. Biol. Chem., 277, 45028-45033.
39. Gomez-del Arco,P., Maki,K. and Georgopoulos,K. (2004) Phosphorylation controls Ikaros's ability to negatively regulate the G(1)-S transition. Mol. Cell. Biol., 24, 2797-2807.
40. Tabach,Y., Milyavsky,M., Shats,I., Brosh,R., Zuk,O., Yitzhaky,A., Mantovani,R., Domany,E., Rotter,V. et al. (2005) The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol. Syst. Biol., 1 2005-2022.
41. Osterloh,L., von Eyss,B., Schmit,F., Rein,L., Hubner,D., Samans,B., Hauser,S. and Gaubatz,S. (2007) The human synMuv-like protein LIN-9 is required for transcription of G2/M genes and for entry into mitosis. EMBO J., 26, 144-157.
42. Zhu,W., Giangrande,P.H. and Nevins,J.R. (2004) E2Fs link the control of G1/S and G2/M transcription. EMBO J., 23, 4615-4626.
43. Wu,F. and Lee,A.S. (2002) CDP and AP-2 mediated repression mechanism of the replication-dependent hamster historic H3.2 promoter. J. Cell Biochem., 84, 699-707.
44. Park,S.H., Wiwi,C.A. and Waxman,D.J. (2006) Signalling cross-talk between hepatocyte nuclear factor 4alpha and growth-hormone-activated STAT5b. Biochem. J., 397, 159-168.
45. Schuh,A.H., Tipping,A.J., Clark,A.J., Hamlett,I., Guyot,B., Iborra,F.J., Rodriguez,P., Strouboulis,J., Enver,T. et al. (2005) ETO-2 associates with SCL in erythroid cells and megakaryocytes and provides repressor functions in erythropoiesis. Mol. Cell. Biol., 25, 10235-10250.
46. Lee,H.J., Oh,Y.K., Rhee,M., Lim,J.Y., Hwang,J.Y., Park,Y.S., Kwon,Y., Choi,K.H., Jo,I. et al. (2007) The role of STAT1/IRF-1 on synergistic ros production and loss of mitochondrial transmembrane potential during hepatic cell death induced by LPS/d-GalN. J. Mol. Biol., 369, 967-984.
47. DiMartino,J.F., Selteri,L., Traver,D., Firpo,M.T., Rhee,J., Warnke,R., O'Gorman,S., Weissman,I.L. and Cleary,M.L. (2001) The Hox cofactor and proto-oncogene Pbx1 is required for maintenance of definitive hematopoiesis in the fetal liver. Blood, 98, 618-626.
48. Rodriguez,L., Ochoa,B. and Martinez,M.J. (2007) NF-Y and Sp1 are involved in transcriptional regulation of rat SND p102 gene. Biochem. Biophys. Res. Commun., 356, 226-232.
49. Nakao,K., Miyao,Y., Ohe,Y. and Tamaoki,T. (1989) Involvement of an AFP1-binding site in cell-specific transcription of the pre-S1 region of the human hepatitis B virus surface antigen gene. Nucleic Acids Res. 17, 9833-9842.
50. Latasa,M.U., Couton,D., Charvet,C., Lafanechere,A., Guidotti,J.E., Li,Z., Tuil,D., Daegelen,D., Mitchell,C. et al. (2007) Delayed liver regeneration in mice lacking liver serum response factor. Am. J. Physiol. Gastrointest. Liver Physiol., 292, G996-G1001.
51. Sasaki,T., Suzuki,H., Yagi,K., Furuhashi,M., Yao,R., Susa,S., Noda,T., Arai,Y., Miyazono,K. et al. (2003) Lymphoid enhancer factor 1 makes cells resistant to transforming growth factor beta-induced repression of c-myc. Cancer Res., 63, 801-806.
52. Marten,N.W., Hsiang,C.H., Yu,L., Stollenwerk,N.S. and Straus,D.S. (1999) Functional activity of hepatocyte nuclear factor-1 is specifically decreased in amino acid-limited hepatoma cells. Biochim. Biophys. Acta, 1447, 160-174.
53. Yabuki,T., Ejiri,S. and Tsutsumi,K. (1993) Ubiquitous factors that interact simultaneously with two distinct cis-elements on the rat aldolase B gene promoter. Biochim. Biophys. Acta, 1216, 15-19.
54. Monzen,K., Hiroi,Y., Kudoh,S., Akazawa,H., Oka,T., Takimoto,E., Hayashi,D., Hosoda,T., Kawabata,M. et al. (2001) Smads, TAK1, and their common target ATF-2 play a critical role in cardiomyocyte differentiation. J. Cell Biol., 153, 687-698.
55. Motoyama,K., Fukumoto,S., Koyama,H., Emoto,M., Shimano,H., Maemura,K. and Nishizawa,Y. (2006) SREBP inhibits VEGF expression in human smooth muscle cells. Biochem. Biophys. Res. Commun., 342, 354-360.
56. Schwarzkopf,M., Coletti,D., Sassoon,D. and Marazzi,G. (2006) Muscle cachexia is regulated by a p53-PW1/Peg3-dependent pathway. Genes Dev. 20, 3440-3452.
57. Berkes,C.A., Bergstrom,D.A., Penn,B.H., Seaver,K.J., Knoepfler,P.S. and Tapscott,S.J. (2004) Pbx marks genes for activation by MyoD indicating a role for a homeodomain protein in establishing myogenic potential. Mol. Cell, 14, 465-477.
58. Pownall,M.E., Gustafsson,M.K., Emerson,C.P. and jr (2002) Myogenic regulatory factors and the specification of muscle progenitors in vertebrate embryos. Annu. Rev. Cell Dev. Biol., 18, 747-783.
59. Funk,W.D. and Wright,W.E. (1992) Cyclic amplification and selection of targets for multicomponent complexes: Myogenin interacts with factors recognizing binding sites for basic helix-loop-helix, nuclear factor 1, myocyte-specific enhancer-binding factor 2, and COMP1 factor. Proc. Natl Acad. Sci. USA, 89, 9484-9488.