Systematic identification of yeast cell cycle transcription factors using multiple data sources

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Wu, Wei Sheng ^a   Li, Wen Hsiung ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b BIODIVERSITY RESEARCH CENTER   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX BIOLOGICAL SYSTEMS; COMPUTATIONAL STUDIES; EUKARYOTIC CELL CYCLE; GENE EXPRESSION DATASETS; MULTIPLE DATA SOURCES; REGULATORY RELATIONSHIPS; SYSTEMATIC IDENTIFICATION; TRANSCRIPTION FACTOR BINDING SITES;

FORECASTING; MATRIX ALGEBRA; TRANSCRIPTION FACTORS;

GENES;

TRANSCRIPTION FACTOR;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CELL CYCLE; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; PHYSIOLOGY; YEAST;

CELL CYCLE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, FUNGAL; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION FACTORS; YEASTS;

EID: 58149333393     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-522     Document Type: Article

References (48)

1. Rowicka M Kudlicki A Tu BP Otwinowski Z High-resolution timing of cell cycle-regulated gene expression Proc Natl Acad Sci USA 2007, 104(43):16892-16897. 2040468 17827275 10.1073/pnas.0706022104
2. 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, 9:3273-3297. 25624 9843569
3. 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, 106:697-708. 10.1016/S0092-8674(01)00494-9 11572776
4. 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
5. Ihmels J Friedlander G Bergmann S Sarig O Ziv Y Barkai N Revealing modular organization in the yeast transcriptional network Nat Genet 2002, 31:370-377. 12134151
6. Pilpel Y Sudarsanam P Church GM Identifying regulatory networks by combinatorial analysis of promoter elements Nat Genet 2001, 29:153-159. 10.1038/ng724 11547334
7. 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, 298:799-804. 10.1126/science.1075090 12399584
8. 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, 431:99-104. 10.1038/nature02800 15343339
9. MacIsaac KD Wang T Gordon DB Gifford DK Stormo GD Fraenkel E An improved map of conserved regulatory sites for Saccharomyces cerevisiae BMC Bioinformatics 2006, 7:113. 1435934 16522208 10.1186/1471-2105-7-113
10. Teixeira MC Monteiro P Jain P Tenreiro S Fernandes AR Mira NP Alenquer M Freitas AT Oliveira AL Sá-Correia I The YEASTRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae Nucl Acids Res 2006, 34:D446-D451. 1347376 16381908 10.1093/nar/gkj013
11. Mewes HW Frishman D Guldener U Mannhaupt G Mayer K Mokrejs M Morgenstern B Munsterkotter M Rudd S Weil B MIPS: A database for genomes and protein sequences Nucleic Acids Res 2002, 30:31-34. 99165 11752246 10.1093/nar/ 30.1.31
12. Tsai HK Lu HH Li WH Statistical methods for identifying yeast cell cycle transcription factors Proc Natl Acad Sci USA 2005, 102:12532-12537. 1224643 16157877 10.1073/pnas.0505874102
13. 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
14. Cheng C Li LM Systematic identification of cell cycle regulated transcription factors from microarray time series data BMC Genomics 2008, 9:116. 2315658 18315882 10.1186/1471-2164-9-116
15. de Lichtenberg U Jensen LJ Fausbøll A Jensen TS Bork P Brunak S Comparison of computational methods for the identification of cell cycle-regulated genes Bioinformatics 2005, 21(7):1164-1171. 10.1093/ bioinformatics/bti093 15513999
16. McBride HJ Yu Y Stillman DJ Distinct regions of the Swi5 and Ace2 transcription factors are required for specific gene activation J Biol Chem 1999, 274:21029-21036. 10.1074/jbc.274.30.21029 10409653
17. Pramila T Miles S GuhaThakurta D Jemiolo D Breeden LL Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle Genes Dev 2002, 16:3034-3045. 187489 12464633 10.1101/gad.1034302
18. McInerny CJ Partridge JF Mikesell GE Creemer DP Breeden LL A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription Genes Dev 1997, 11:1277-1288. 10.1101/gad.11.10.1277 9171372
19. Koch C Nasmyth K Cell cycle regulated transcription in yeast Curr Opin Cell Biol 1994, 6:451-459. 10.1016/0955-0674(94)90039-6 7917338
20. Futcher B Transcriptional regulatory networks and the yeast cell cycle Curr Opin Cell Biol 2002, 14:676-683. 10.1016/S0955-0674(02)00391-5 12473339
21. Koranda M Schleiffer A Endler L Ammerer G Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters Nature 2000, 406:94-98. 10.1038/35017589 10894549
22. Kumar R Reynolds DM Shevchenko A Shevchenko A Goldstone SD Dalton S Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase Curr Biol 2000, 10:896-906. 10.1016/S0960-9822(00)00618-7 10959837
23. Cherry JM Adler C Ball C Chervitz SA Dwight SS Hester ET Jia Y Juvik G Roe T Schroeder M Weng S Botstein D SGD: Saccharomyces Genome Database Nucleic Acids Res 1998, 26(1):73-80. 147204 9399804 10.1093/nar/26.1.73
24. Banerjee N Zhang MQ Identifying cooperativity among transcription factors controlling the cell cycle in yeast Nucleic Acids Res 2003, 31:7024-7031. 290262 14627835 10.1093/nar/gkg894
25. 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, 21:1337-1342. 10.1038/nbt890 14555958
26. Kato M Hata N Banerjee N Futcher B Zhang MQ Identifying combinatorial regulation of transcription factors and binding motifs Genome Biology 2004, 5:R56. 507881 15287978 10.1186/gb-2004-5-8-r56
27. Gao F Foat BC Bussemaker HJ Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data BMC Bioinformatics 2004, 5(1):31. 407845 15113405 10.1186/ 1471-2105-5-31
28. Wu WS Li WH Chen BS Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data BMC Bioinformatics 2007, 8:188. 1906835 17559637 10.1186/1471-2105-8-188
29. Kato M Tsunoda T Takagi T Lag analysis of genetic networks in the cell cycle of budding yeast Genome Inform 2001, 12:266-267.
30. Reis BY Butte AJ Kohane IS Approaching causality: Discovering time-lag correlations in genetic expression data with static and dynamic relevance networks RECOMB 2000, 5.
31. Schmitt WAJr Raab RM Stephanopoulos G Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data Genome Res 2004, 14:1654-1663. 509275 15289483 10.1101/gr.2439804
32. Liping J Tan KL Identifying time-lagged gene clusters using gene expression data Bioiformatics 2005, 21:509-516. 10.1093/bioinformatics/ bti1058
33. Qian J Dolled-Filhart M Lin J Yu H Gerstein M Beyond synexpression relationships: Local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions J Mol Biol 2001, 314:1053-1066. 10.1006/jmbi.2000.5219 11743722
34. Liao JC Boscolo R Yang YL Tran LM Sabatti C Roychowdhury VP Network component analysis: Reconstruction of regulatory signals in biological system Proc Natl Acad Sci USA 2003, 100:15522-15527. 307600 14673099 10.1073/pnas.2136632100
35. Yu T Li KC Inference of transcriptional regulatory network by two-stage constrained space factor analysis Bioinformatics 2005, 21:4033-4038. 10.1093/bioinformatics/bti656 16144806
36. Zhou XJ Kao MC Huang H Wong A Nunez-Iglesias J Primig M Aparicio OM Finch CE Morgan TE Wong WHZ Functional annotation and network reconstruction through cross-platform integration of microarray data Nat Biotechnol 2005, 23:238-243. 10.1038/nbt1058 15654329
37. Cokus S Rose S Haynor D Grønbech-Jensen N Pellegrini M Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae BMC Bioinformatics 2006, 7:381. 1570153 16914048 10.1186/1471-2105-7-381
38. Andersson CR Hvidsten TR Isaksson A Gustafsson MG Komorowski J Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors BMC Syst Biol 2007, 1:45. 2200664 17939860 10.1186/1752-0509-1-45
39. 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 Biol 2006, 7(5):R37. 1779513 16677396 10.1186/gb-2006-7-5-r37
40. Shakhnovich BE Reddy TE Galinsky K Mellor J Delisi C Comparisons of predicted genetic modules: Identification of co-expressed genes through module gene flow Genome Inform Ser Workshop Genome Inform 2004, 15:221-228.
41. Pramila T Wu W Miles S Noble WS Breeden LL The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle Genes Dev 2006, 20(16):2266-2278. 1553209 16912276 10.1101/gad.1450606
42. Faires JD Burden R Numerical Methods Pacific Grove: Brooks/Cole Publishing Company 2, 1998.
43. Johansson R System modeling and identification Englewood Cliffs: Prentice-Hall 1993.
44. Chang YH Wang YC Chen BS Identification of transcription factor cooperativity via stochastic system model Bioinformatics 2006, 22(18):2276-2282. 10.1093/bioinformatics/btl380 16844711
45. Wu WS Li WH Identifying gene regulatory modules of heat shock response in yeast BMC Genomics 2008, 9:439. 2575218 18811975 10.1186/ 1471-2164-9-439
46. Mendenhall W Sincich T Statistics for Engineering and the Sciences Englewood Cliffs: Prentice-Hall 4, 1995.
47. Wu WS Chen BS Identifying stress transcription factors using gene expression and TF-gene association data Bioinformatics and Biology Insights 2007, 1:9-17.
48. Wu X Zhu L Guo J Fu C Zhou H Dong D Li Z Zhang DY Lin K SPIDer: Saccharomyces protein-protein interaction database BMC Bioinformatics 2006, 7:S16. 1764472 17254300 10.1186/1471-2105-7-S5-S16