GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Shen, Li ^a   Liu, Jie ^a   Wang, Wei ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CO-REGULATED GENES; CRITICAL STEPS; DNA MOTIF; GENE EXPRESSION PATTERNS; GIBBS SAMPLERS; REGULATION OF TRANSCRIPTION; REGULATORY RULES; TRANSCRIPTIONAL REGULATION;

GENE EXPRESSION;

BAYESIAN NETWORKS;

DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR E2F; TRANSCRIPTION FACTOR YYI; UNCLASSIFIED DRUG; PROTEOME;

ARTICLE; BAYES THEOREM; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENETIC DATABASE; HUMAN; NONHUMAN; PROTEIN BINDING; SIMULATION; TRANSCRIPTION REGULATION; YEAST; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; METABOLISM; METHODOLOGY; MULTIGENE FAMILY; PHYSIOLOGY; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION;

BAYES THEOREM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; MULTIGENE FAMILY; PROTEOME; SIGNAL TRANSDUCTION; SOFTWARE; TRANSCRIPTIONAL ACTIVATION;

EID: 53749099767     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-395     Document Type: Article

References (38)

1. Tompa M Li N Bailey TL Church GM De Moor B Eskin E Favorov AV Frith MC Fu Y Kent WJ Assessing computational tools for the discovery of transcription factor binding sites Nat Biotechnol 2005, 23(1):137-144. 10.1038/nbt1053 15637633
2. Mukherjee S Berger MF Jona G Wang XS Muzzey D Snyder M Young RA Bulyk ML Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays Nat Genet 2004, 36(12):1331-1339. 10.1038/ng1473 15543148
3. Levine M Tjian R Transcription regulation and animal diversity Nature 2003, 424:147-151. 10.1038/nature01763 12853946
4. Yu X Lin J Masuda T Esumi N Zack DJ Qian J Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae Nucleic Acids Research 2006, 34(3):917-927. 1361616 16464824 10.1093/nar/gkj487
5. Yu X Lin J Zack DJ Qian J Computational analysis of tissue-specific combinatorial gene regulation: Predicting interaction between transcription factors in human tissues Nucleic Acids Res 2006, 34(17):4925-4936. 1635265 16982645 10.1093/nar/gkl595
6. Bulyk ML McGuire AM Masuda N Church GM A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli Genome Res 2004, 14(2):201-208. 327095 14762058 10.1101/ gr.1448004
7. Hannenhalli S Levy S Predicting transcription factor synergism Nucleic Acids Res 2002, 30(19):4278-4284. 140535 12364607 10.1093/nar/gkf535
8. Pilpel Y Sudarsanam P Church GM Identifying regulatory networks by combinatorial analysis of promoter elements Nat Genet 2001, 29(2):153-159. 10.1038/ng724 11547334
9. Zhu Z Shendure J Church GM Discovering functional transcription-factor combinations in the human cell cycle Genome Research 2005, 15:848-855. 1142475 15930495 10.1101/gr.3394405
10. Banerjee N Zhang MQ Identifying cooperativity among transcription factors controlling the cell cycle in yeast Nucleic Acids Res 2003, 31(23):7024-7031. 290262 14627835 10.1093/nar/gkg894
11. Kato M Hata N Banerjee N Futcher B Zhang MQ Identifying combinatorial regulation of transcription factors and binding motifs Genome Biology 2004, 5:8. 15287978
12. Das D Banerjee N Zhang MQ Interacting models of cooperative gene regulation PNAS 2004, 101(46):16234-16239. 528978 15534222 10.1073/ pnas.0407365101
13. Segal E Shapira M Regev A Pe'er D Botstein D Koller D Friedman N Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data Nat Genet 2003, 34(2):166-176. 10.1038/ng1165 12740579
14. Kulkarni MM Arnosti DN cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster Mol Cell Biol 2005, 25(9):3411-3420. 1084297 15831448 10.1128/MCB.25.9.3411-3420.2005
15. Elemento O Slonim N Tavazoie S A universal framework for regulatory element discovery across all genomes and data types Mol Cell 2007, 28(2):337-350. 10.1016/j.molcel.2007.09.027 17964271
16. Beer M Tavazoie S Predicting gene expression from sequence Cell 2004, 117:185-198. 10.1016/S0092-8674(04)00304-6 15084257
17. Yuan Y Guo L Shen L Liu JS Predicting Gene Expression from Sequence: A Reexamination PLoS Computational Biology 2007, 3(11):e243. 2098866 18052544 10.1371/journal.pcbi.0030243
18. Austen M Luscher B Luscher-Firzlaff JM Characterization of the Transcriptional Regulator YY1 J Biol Chem 1997, 272(3):1709-1717. 10.1074/jbc.272.3.1709 8999850
19. Shi Y Lee J-S Galvin KM Everything you have ever wanted to know about Yin Yang 1 Biochimica et Biophysica Acta (BBA) - Reviews on Cancer 1997, 1332(2):F49-F66. 9141463 10.1016/S0304-419X(96)00044-3
20. Gordon S Akopyan G Garban H Bonavida B Transcription factor YY1: structure, function, and therapeutic implications in cancer biology Oncogene 2005, 25(8):1125-1142. 16314846 10.1038/sj.onc.1209080
21. Shen L Wang K Liu J Affar EB Shi Y Ren B Wang W Rewiring of the YY1 transcriptional program in human and mouse 2008.
22. Wang W Cherry JM Nochomovitz Y Jolly E Botstein D Li H Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation Proceedings of the National Academy of Sciences 2005, 102(6):1998-2003. 15684073 10.1073/pnas.0405537102
23. Su A Wiltshire T Batalov S Lapp H Ching K Block D Zhang J Soden R Hayakawa M Kreiman G HG_U133A/GNF1H and GNF1M Tissue Atlas Datasets Proc Natl Acad Sci USA 2004, 101(16):6062-6067. 395923 15075390 10.1073/ pnas.0400782101
24. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998, 95:14863-14868. 24541 9843981 10.1073/pnas.95.25.14863
25. Matys V Fricke E Geffers R Gossling E Haubrock M Hehl R Hornischer K Karas D Kel AE Kel-Margoulis OV TRANSFAC: Transcriptional regulation, from patterns to profiles Nucleic Acids Res 2003, 31(1):374-378. 165555 12520026 10.1093/nar/gkg108
26. Fisher RA Statistical Methods for research workers Oliver and Boyd 1954.
27. Liu X Brutlag D Liu J BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes Pac Symp Biocomput: 2001 2001:127-138. 11262934
28. Presnell SR Zhang L Ramilo CA Chan HW Lutz CT Functional redundancy of transcription factor-binding sites in the killer cell Ig-like receptor (KIR) gene promoter Int Immunol 2006, 18(8):1221-1232. 10.1093/intimm/ dxl043 16818466
29. Patton J Block S Coombs C Martin ME Identification of functional elements in the murine Gabp alpha/ATP synthase coupling factor 6 bi-directional promoter Gene 2006, 369:35-44. 10.1016/j.gene.2005.10.009 16309857
30. Schlisio S Halperin T Vidal M Nevins JR Interaction of YY1 with E2Fs, mediated by RYBP, provides a mechanism for specificity of E2F function Embo J 2002, 21(21):5775-5786. 131074 12411495 10.1093/emboj/cdf577
31. Wu S Murai S Kataoka K Miyagishi M Cooperative regulation of p73 promoter by Yin Yang 1 and E2F1 Nucleic Acids Symp Ser (Oxf) 2007, 51:347-348. 10.1093/nass/nrm174 18029729
32. Chang MS Yoo HY Rho HM Positive and negative regulatory elements in the upstream region of the rat Cu/Zn-superoxide dismutase gene Biochem J 1999, 339(Pt 2):335-341. 1220162 10191264 10.1042/0264-6021:3390335
33. Srivastava S Chandrasekar B Gu Y Luo J Hamid T Hill BG Prabhu SD Downregulation of CuZn-superoxide dismutase contributes to [beta]-adrenergic receptor-mediated oxidative stress in the heart Cardiovascular Research 2007, 74(3):445-455. 10.1016/ j.cardiores.2007.02.016 17362897
34. Xu X Bieda M Jin VX Rabinovich A Oberley MJ Green R Farnham PJ A comprehensive ChIP chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members Genome Res 2007. gr.6783507 2045138 17908821
35. Heintzman ND Stuart RK Hon G Fu Y Ching CW Hawkins RD Barrera LO Van Calcar S Qu C Ching KA Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nat Genet 2007, 39(3):311-318. 10.1038/ng1966 17277777
36. Hallikas O Palin K Sinjushina N Rautiainen R Partanen J Ukkonen E Taipale J Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity Cell 2006, 124(1):47-59. 10.1016/j.cell.2005.10.042 16413481
37. Kim TH Barrera LO Zheng M Qu C Singer MA Richmond TA Wu Y Green RD Ren B A high-resolution map of active promoters in the human genome Nature 2005, 436(7052):876-880. 1895599 15988478 10.1038/nature03877
38. Kim TH Barrera LO Ren B ChIP-chip for Genome-Wide Analysis of Protein Binding in Mammalian Cells Current Protocols in Molecular Biology 2007, 79:21-21. 18265397