Transcriptional programs: Modelling higher order structure in transcriptional control

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Reid, John E ^a   Ott, Sascha ^b   Wernisch, Lorenz ^a  

^a MRC BIOSTATISTICS UNIT   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HIGHER-ORDER STRUCTURE; NON-PARAMETRIC PROBABILISTIC MODELS; TRANSCRIPTION FACTOR BINDING; TRANSCRIPTIONAL CONTROL; TRANSCRIPTIONAL MODULES; TRANSCRIPTIONAL PROGRAM; TRANSCRIPTIONAL REGULATION; TRANSCRIPTIONAL REGULATORY SYSTEM;

GENES;

TRANSCRIPTION FACTORS;

TRANSCRIPTION FACTOR;

ARTICLE; BIOINFORMATICS; GENE CONTROL; GENE SEQUENCE; INFORMATION RETRIEVAL; NONHUMAN; PREDICTION; PROMOTER REGION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; ANIMAL; BINDING SITE; BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MOUSE;

EUKARYOTA; MUS MUSCULUS;

ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MICE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 68949162986     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-218     Document Type: Article

References (33)

1. Ingham PW The molecular genetics of embryonic pattern formation in Drosophila Nature 1988, 335(6185):25-34. 10.1038/335025a0 2901040
2. Arnosti DN Kulkarni MM Transcriptional enhancers: Intelligent enhanceosomes or exible billboards? J Cell Biochem 2005, 94(5):890-898. 10.1002/jcb.20352 15696541
3. Simmons DM Voss JW Ingraham HA Holloway JM Broide RS Rosenfeld MG Swanson LW Pituitary cell phenotypes involve cell-specific Pit-1 mRNA translation and synergistic interactions with other classes of transcription factors Genes Dev 1990, 4(5):695-711. 10.1101/gad.4.5.695 2379827
4. Matys V Fricke E Geffers R Gössling E Haubrock M Hehl R Hornischer K Karas D Kel AE Kel-Margoulis OV Kloos DU Land S Lewicki-Potapov B Michael H Munch R Reuter I Rotert S Saxel H Scheer M Thiele S Wingender E TRANSFAC: Transcriptional regulation, from patterns to profiles Nucleic Acids Res 2003, 31:374-378. 165555 12520026 10.1093/nar/gkg108
5. Sandelin A Alkema W Engström P Wasserman WW Lenhard B JASPAR: An open-access database for eukaryotic transcription factor binding profiles Nucleic Acids Res 2004, 32(Database):D91-D94. 308747 14681366 10.1093/nar/gkh012
6. Teh YW Jordan MI Beal MJ Blei DM Hierarchical Dirichlet Processes Journal of the American Statistical Association 2006, 101(476):1566-1581. 10.1198/016214506000000302
7. Sharan R Ben-Hur A Loots GG Ovcharenko I CREME: Cis-Regulatory Module Explorer for the human genome Nucleic Acids Res 2004, 32(Web Server):W253-W256. 441523 15215390 10.1093/nar/gkh385
8. Ho Sui SJ Fulton DL Arenillas DJ Kwon AT Wasserman WW oPOSSUM: integrated tools for analysis of regulatory motif over-representation Nucleic Acids Res 2007, 35(Web Server):W245-W252. 1933229 17576675 10.1093/nar/gkm427
9. Kreiman G Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes Nucleic Acids Res 2004, 32:2889-2900. 419615 15155858 10.1093/nar/gkh614
10. Singh LN Wang LS Hannenhalli S TREMOR - a tool for retrieving transcriptional modules by incorporating motif covariance Nucleic Acids Res 2007, 35(21):7360-7371. 2189735 17962303 10.1093/nar/gkm885
11. Lemmens K Dhollander T Bie TD Monsieurs P Engelen K Smets B Winderickx J Moor BD Marchal K Inferring transcriptional modules from ChIP-chip, motif and microarray data Genome Biol 2006, 7(5):R37. 1779513 16677396 10.1186/gb-2006-7-5-r37
12. Chen G Jensen ST Stoeckert CJ Clustering of genes into regulons using integrated modeling-COGRIM Genome Biol 2007, 8:R4. 1839128 17204163 10.1186/gb-2007-8-1-r4
13. Jensen ST Chen G Stoeckert CJ Bayesian variable selection and data integration for biological regulatory networks ANNALS OF APPLIED STATISTICS 2007, 1:612. 10.1214/07-AOAS130
14. Tanay A Sharan R Kupiec M Shamir R Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data Proc Natl Acad Sci USA 2004, 101(9):2981-2986. 365731 14973197 10.1073/pnas.0308661100
15. Blüthgen N Kie Ibasa SM Herzel H Inferring combinatorial regulation of transcription in silico Nucleic Acids Res 2005, 33:272-279. 546154 15647509 10.1093/nar/gki167
16. Frith MC Li MC Weng Z Cluster-Buster: Finding dense clusters of motifs in DNA sequences Nucleic Acids Res 2003, 31(13):3666-3668. 168947 12824389 10.1093/nar/gkg540
17. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25:25-29. 10.1038/75556 10802651
18. Wu WS Li WH Chen BS Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle BMC Bioinformatics 2006, 7:421. 1637117 17010188 10.1186/1471-2105-7-421
19. Segal E Yelensky R Koller D Genome-wide discovery of transcriptional modules from DNA sequence and gene expression Bioinformatics 2003, 19(Suppl 1):i273-i282. 10.1093/bioinformatics/btg1038 12855470
20. Xu X Wang L Ding D Learning module networks from genome-wide location and expression data FEBS Lett 2004, 578(3):297-304. 10.1016/ j.febslet.2004.11.019 15589836
21. 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
22. Gerber GK Dowell RD Jaakkola TS Gifford DK Automated discovery of functional generality of human gene expression programs PLoS Comput Biol 2007, 3(8):e148. 1941755 17696603 10.1371/journal.pcbi.0030148
23. Liu X Jessen WJ Sivaganesan S Aronow BJ Medvedovic M Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data BMC Bioinformatics 2007, 8:283. 1994961 17683565 10.1186/1471-2105-8-283
24. Kanehisa M Goto S Hattori M Aoki-Kinoshita KF Itoh M Kawashima S Katayama T Araki M Hirakawa M From genomics to chemical genomics: New developments in KEGG Nucleic Acids Res 2006, 34(Database):D354-D357. 1347464 16381885 10.1093/nar/gkj102
25. Su AI Cooke MP Ching KA Hakak Y Walker JR Wiltshire T Orth AP Vega RG Sapinoso LM Moqrich A Patapoutian A Hampton GM Schultz PG Hogenesch JB Large-scale analysis of the human and mouse transcriptomes Proc Natl Acad Sci USA 2002, 99(7):4465-4470. 123671 11904358 10.1073/ pnas.012025199
26. Alexa A Rahnenführer J Lengauer T Improved scoring of functional groups from gene expression data by decorrelating GO graph structure Bioinformatics 2006, 22(13):1600-1607. 10.1093/bioinformatics/btl140 16606683
27. Elkon R Linhart C Sharan R Shamir R Shiloh Y Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells Genome Res 2003, 13(5):773-780. 430898 12727897 10.1101/ gr.947203
28. Lichtlen P Wang Y Belser T Georgiev O Certa U Sack R Schaffner W Target gene search for the metal-responsive transcription factor MTF-1 Nucleic Acids Res 2001, 29(7):1514-1523. 31279 11266553 10.1093/nar/29.7.1514
29. Joshi B Ordonez-Ercan D Dasgupta P Chellappan S Induction of human metallothionein 1G promoter by VEGF and heavy metals: Differential involvement of E2F and metal transcription factors Oncogene 2005, 24(13):2204-2217. 10.1038/sj.onc.1208206 15735762
30. Kent WJ Sugnet CW Furey TS Roskin KM Pringle TH Zahler AM Haussler D The human genome browser at UCSC Genome Res 2002, 12(6):996-1006. 186604 12045153
31. Hubbard TJ Aken BL Beal K Ballester B Caccamo M Chen Y Clarke L Coates G Cunningham F Cutts T Down T Dyer SC Fitzgerald S Fernandez-Banet J Graf S Haider S Hammond M Herrero J Holland R Howe K Howe K Johnson N Kahari A Keefe D Kokocinski F Kulesha E Lawson D Longden I Melsopp C Megy K Meidl P Ouverdin B Parker A Prlic A Rice S Rios D Schuster M Sealy I Severin J Slater G Smedley D Spudich G Trevanion S Vilella A Vogel J White S Wood M Cox T Curwen V Durbin R Fernandez-Suarez XM Flicek P Kasprzyk A Proctor G Searle S Smith J Ureta-Vidal A Birney E Ensembl 2007 Nucleic Acids Res 2007, 35(Database):D610-D617. 1761443 17148474 10.1093/nar/gkl996
32. Teh YW Kurihara K Welling M Collapsed Variational Inference for HDP Advances in Neural Information Processing Systems 2008, 20. 2600676 19079779
33. Sethuraman J A constructive definition of Dirichlet priors Statistica Sinica 1994, 4:639-650.