Prioritization of gene regulatory interactions from large-scale modules in yeast

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Lee, Ho Joon ^a   Manke, Thomas ^a   Bringas, Ricardo ^a   Vingron, Martin ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELL WALL SYNTHESIS; CO-REGULATED GENES; COMPLEMENTARY SETS; EXPERIMENTAL VERIFICATION; PREDICTION ACCURACY; REGULATORY INTERACTIONS; REGULATORY PROTEIN; TRANSCRIPTIONAL MODULES;

BIOSYNTHESIS; SET THEORY; TRANSCRIPTION FACTORS; YEAST;

GENES;

CELL MEMBRANE PROTEIN; GLYCOPROTEIN; GLYCOPROTEIN CIS3; MINICHROMOSOME MAINTENANCE PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FKH2; TRANSCRIPTION FACTOR NDD1; TRANSCRIPTION FACTOR SWI4; TRANSCRIPTION FACTOR SWI6; UNCLASSIFIED DRUG; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BINDING SITE; CELL WALL; COMPLEX FORMATION; CONTROLLED STUDY; DATA ANALYSIS; FUNGAL GENETICS; FUNGUS GROWTH; GENE EXPRESSION; GENE FUNCTION; GENE INTERACTION; GENE TARGETING; GENETIC REGULATION; GENOME ANALYSIS; NONHUMAN; PREDICTION; PROTEIN SYNTHESIS REGULATION; SENSITIVITY AND SPECIFICITY; TRANSCRIPTION REGULATION; YEAST; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; METABOLISM; METHODOLOGY; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

ALGORITHMS; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 39149128781     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-32     Document Type: Article

References (37)

1. Bar-Joseph Z Gerber GK Lee TI Rinaldi NJ Yoo JY Robert F Gordon DB Fraenkel E Jaakkola TS Young RA Gifford DK Computational discovery of gene modules and regulatory networks Nat Biotechnol 2003, 21(11):1337-1342. 10.1038/nbt890 14555958
2. Ihmels J Friedlander G Bergmann S Sarig O Ziv Y Barkai N Revealing modular organization in the yeast transcriptional network Nat Genet 2002, 31(4):370-377. 12134151
3. 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. 12740579
4. 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
5. 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
6. Yu T Li KC Inference of transcriptional regulatory network by two-stage constrained space factor analysis Bioinformatics 2005, 21(21):4033-4038. 10.1093/bioinformatics/bti656 16144806
7. Lemmens K Dhollander T De Bie T Monsieurs P Engelen K Smets B Winderickx J De Moor B Marchal K Inferring transcriptional modules from ChIP-chip, motif and microarray data Genome Biology 2006, 7(5):R37. 1779513 16677396 10.1186/gb-2006-7-5-r37
8. Wu W-S Li W-H Chen B-S Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle BMC Bioinformatics 2006, 7(1):421. 1637117 17010188 10.1186/1471-2105-7-421
9. Gao F Foat BC Bussemaker HJ Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data BMC Bioinformatics 2004, 5:31. 407845 15113405 10.1186/ 1471-2105-5-31
10. Hartwell LH Hopfield JJ Leibler S Murray AW From molecular to modular cell biology Nature 1999, 402(6761 Suppl):C47-52. 10.1038/35011540 10591225
11. Barabasi A-L Oltvai ZN Network biology: Understanding the cell's functional organization Nat Rev Genet 2004, 5(2):101-113. 10.1038/ nrg1272 14735121
12. Manke T Bringas R Vingron M Correlating protein-DNA and protein-protein interaction networks J Mol Biol 2003, 333(1):75-85. 10.1016/ j.jmb.2003.08.004 14516744
13. Lee TI Rinaldi NJ Robert F Odom DT Bar-Joseph Z Gerber GK Hannett NM Harbison CT Thompson CM Simon I Zeitlinger J Jennings EG Murray HL Gordon DB Ren B Wyrick JJ Tagne JB Volkert TL Fraenkel E Gifford DK Young RA Transcriptional regulatory networks in Saccharomyces cerevisiae Science 2002, 298(5594):799-804. 10.1126/science.1075090 12399584
14. Spellman PT Sherlock G Zhang MQ Iyer VR Anders K Eisen MB Brown PO Botstein D Futcher B Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol Biol Cell 1998, 9(12):3273-3297. 25624 9843569
15. Mewes HW Amid C Arnold R Frishman D Guldener U Mannhaupt G Munsterkotter M Pagel P Strack N Stumpflen V Warfsmann J Ruepp A MIPS: Analysis and annotation of proteins from whole genomes Nucleic Acids Res 2004, 32(Database):D41-44. 308826 14681354 10.1093/nar/gkh092
16. Harbison CT Gordon DB Lee TI Rinaldi NJ Macisaac KD Danford TW Hannett NM Tagne JB Reynolds DB Yoo J Jennings EG Zeitlinger J Pokholok DK Kellis M Rolfe PA Takusagawa KT Lander ES Gifford DK Fraenkel E Young RA Transcriptional regulatory code of a eukaryotic genome Nature 2004, 431(7004):99-104. 10.1038/nature02800 15343339
17. Greenbaum D Jansen R Gerstein M Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts Bioinformatics 2002, 18(4):585-596. 10.1093/bioinformatics/18.4.585 12016056
18. Prochasson P Florens L Swanson SK Washburn MP Workman JL The HIR corepressor complex binds to nucleosomes generating a distinct protein/ DNA complex resistant to remodeling by SWI/SNF Genes Dev 2005, 19(21):2534-2539. 1276727 16264190 10.1101/gad.1341105
19. Schweizer E Hofmann J Microbial Type I Fatty Acid Synthases (FAS): Major Players in a Network of Cellular FAS Systems Microbiol Mol Biol Rev 2004, 68(3):501-517. 515254 15353567 10.1128/MMBR.68.3.501-517.2004
20. Lesage G Bussey H Cell Wall Assembly in Saccharomyces cerevisiae Microbiol Mol Biol Rev 2006, 70(2):317-343. 1489534 16760306 10.1128/ MMBR.00038-05
21. Zhang N Gardner D Oliver S Stateva L Down-regulation of the expression of PKC1 and SRB1/PSA1/VIG9, two genes involved in cell wall integrity in Saccharomyces cerevisiae, causes flocculation Microbiology 1999, 145(2):309-316. 10075413
22. Rolland F Winderickx J Thevelein JM Glucose-sensing and -signalling mechanisms in yeast FEMS Yeast Research 2002, 2(2):183-201. 12702307
23. Newcomb LL Diderich JA Slattery MG Heideman W Glucose Regulation of Saccharomyces cerevisiae Cell Cycle Genes Eukaryotic Cell 2003, 2(1):143-149. 141163 12582131 10.1128/EC.2.1.143-149.2003
24. Rahmann S Muller T Vingron M On the power of profiles for transcription factor binding site detection Stat Appl Genet Mol Biol 2003, 2(1): Article 7. 16646785
25. Saccharomyces Genome Database (SGD) ftp://ftp.yeastgenome.org/yeast/ http://www.yeastgenome.org/
26. Koranda M Schleiffer A Endler L Ammerer G Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters 2000, 406(6791):94-98. 10894549
27. Iyer VR Horak CE Scafe CS Botstein D Snyder M Brown PO Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature 2001, 409(6819):533-538. 10.1038/35054095 11206552
28. Simon I Barnett J Hannett N Harbison CT Rinaldi NJ Volkert TL Wyrick JJ Zeitlinger J Gifford DK Jaakkola TS Young RA Serial regulation of transcriptional regulators in the yeast cell cycle Cell 2001, 106(6):697-708. 10.1016/S0092-8674(01)00494-9 11572776
29. 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
30. Matys V Fricke E Geffers R Gossling 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(1):374-378. 165555 12520026 10.1093/nar/gkg108
31. Siddharthan R Siggia ED van Nimwegen E PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny PLoS Computational Biology 2005, 1(7):e67. 1309704 16477324 10.1371/journal.pcbi.0010067
32. Cliften P Sudarsanam P Desikan A Fulton L Fulton B Majors J Waterston R Cohen BA Johnston M Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting Science 2003, 301(5629):71-76. 10.1126/ science.1084337 12775844
33. Kellis M Patterson N Endrizzi M Birren B Lander E Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003, 423:241-254. 10.1038/nature01644 12748633
34. Doniger SW Huh J Fay JC Identification of functional transcription factor binding sites using closely related Saccharomyces species Genome Res 2005, 15(5):701-709. 1088298 15837806 10.1101/gr.3578205
35. Tavazoie S Hughes JD Campbell MJ Cho RJ Church GM Systematic determination of genetic network architecture Nat Genet 1999, 22(3):281-285. 10.1038/10343 10391217
36. Cytoscape http://www.cytoscape.org/
37. yED graph editor http://www.yWorks.com