Inferring activity changes of transcription factors by binding association with sorted expression profiles

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Cheng, Chao ^a   Yan, Xiting ^a   Sun, Fengzhu ^a   Li, Lei M ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING AFFINITIES; BIOLOGICAL PROCESS; EXPRESSION PROFILE; INFERRING ACTIVITIES; LINEAR RELATIONSHIPS; MICROARRAY EXPRESSIONS; POST-TRANSCRIPTIONAL MODIFICATION; REGULATORY MECHANISM;

GENES; MACHINERY; TRANSCRIPTION; TRANSCRIPTION FACTORS;

BINDING ENERGY;

TRANSCRIPTION FACTOR;

APOPTOSIS; ARTICLE; BINDING ASSAY; BIOLOGICAL ACTIVITY; CELL MATURATION; CELL PROLIFERATION; COMPUTER PROGRAM; DATA ANALYSIS; FUNGUS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE REPRESSION; GENE TARGETING; HUMAN; INFORMATION PROCESSING; LONGEVITY; NONHUMAN; PROTEIN FUNCTION; PROTEIN MICROARRAY; REGULATORY MECHANISM; SIGNAL TRANSDUCTION; ALGORITHM; BINDING SITE; CHEMISTRY; DNA MICROARRAY; DNA SEQUENCE; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; BASE SEQUENCE; BINDING SITES; GENE EXPRESSION PROFILING; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS;

EID: 38049170632     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-452     Document Type: Article

References (48)

1. Bussemaker HJ Li H Siggia ED Regulatory element detection using correlation with expression Nat Genet 2001, 27:167-171. 10.1038/84792 11175784
2. Conlon EM Liu XS Lieb JD Liu JS Integrating regulatory motif discovery and genome-wide expression analysis Proc Natl Acad Sci USA 2003, 100:3339-3344. 152294 12626739 10.1073/pnas.0630591100
3. 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 P 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
4. Liao JC Boscolo R Yang YL Tran LM Sabatti C Roychowdhury VP Network component analysis: Reconstruction of regulatory signals in biological systems Proc Natl Acad Sci USA 2003, 100:15522-15527. 307600 14673099 10.1073/pnas.2136632100
5. Alter O Golub GH Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription Proc Natl Acad Sci USA 2004, 101:16577-16582. 534520 15545604 10.1073/pnas.0406767101
6. 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
7. Boulesteix AL Strimmer K Predicting transcription factor activities from combined analysis of microarray and ChIP data: A partial least squares approach Theor Biol Med Model 2005, 2:23. 1182396 15978125 10.1186/ 1742-4682-2-23
8. Tsai HK Lu HH Li WH Statistical methods for identifying yeast cell cycle transcription factors Proc Natl Acad Sci USA 2005, 102:13532-13537. 1224643 16157877 10.1073/pnas.0505874102
9. Hughes TR Marton MJ Jones AR Roberts CJ Stoughton R Armour CD Bennett HA Coffey E Dai H He YD Kidd MJ King AM Meyer MR Slade D Lum PY Stepaniants SB Shoemaker DD Gachotte D Chakraburtty K Simon J Bard M Friend SH Functional discovery via a compendium of expression profiles Cell 2000, 102:109-126. 10.1016/S0092-8674(00)00015-5 10929718
10. Mnaimneh S Davierwala AP Haynes J Moffat J Peng WT Zhang W Yang X Pootoolal J Chua G Lopez A Trochesset M Morse D Krogan NJ Hiley SL Li Z Morris Q Grigull J Mitsakakis N Roberts CJ Greenblatt JF Boone C Kaiser CA Andrews BJ Hughes TR Exploration of essential gene functions via titratable promoter alleles Cell 2004, 118:31-44. 10.1016/ j.cell.2004.06.013 15242642
11. Gasch A Spellman P Kao C Carmel-Harel O Eisen MB Storz G Botstein D Brown PO Genomic expression programs in the response of yeast cells to environmental changes Mol Biol Cell 2000, 11:4241-4257. 15070 11102521
12. Chua G Morris QD Sopko R Robinson MD Ryan O Chan ET Frey BJ Andrews BJ Boone C Hughes TR Identifying transcription factor functions and targets by phenotypic activation Proc Natl Acad Sci USA 2006, 103:12045-12050. 1567694 16880382 10.1073/pnas.0605140103
13. Hu Z Killion P Iyer V Genetic reconstruction of a functional transcriptional regulatory network Nat Genet 2007, 39:683-687. 10.1038/ ng2012 17417638
14. Spector MS Raff A DeSilva H Lee K Osley MA Hir1p and Hir2p function as transcriptional corepressors to regulate histone gene transcription in the Saccharomyces cerevisiae cell cycle Mol Cell Biol 1997, 17:545-552. 231779 9001207
15. Bean JM Siggia ED Cross FR High functional overlap between MluI cell-cycle box binding factor and Swi4/6 cell-cycle box binding factor in the G1/S transcriptional program in Saccharomyces cerevisiae Genetics 2005, 171:49-61. 1456534 15965243 10.1534/genetics.105.044560
16. Wu X Rossettini A Hanes SD The ESS1 prolyl isomerase and its suppressor BYE1 interact with RNA pol II to inhibit transcription elongation in Saccharomyces cerevisiae Genetics 2003, 165:1687-1702. 1462908 14704159
17. Soussi-Boudekou S Vissers S Urrestarazu A Jauniaux JC Andre B Gzf3p, a fourth GATA factor involved in nitrogen-regulated transcription in Saccharomyces cerevisiae Mol Microbiol 1997, 23:1157-1168. 10.1046/ j.1365-2958.1997.3021665.x 9106207
18. Deckert J Perini R Balasubramanian B Zitomer RS Multiple elements and auto-repression regulate Rox1, a repressor of hypoxic genes in Saccharomyces cerevisiae Genetics 1995, 139:1149-1158. 1206446 7768429
19. Rouillon A Barbey R Patton E Tyers M Thomas D Feedback-regulated degradation of the transcriptional activator Met4 is triggered by the SCF(Met30)complex EMBO J 2000, 19:282-294. 305562 10637232 10.1093/emboj/ 19.2.282
20. Kaiser P Flick K Wittenberg C Reed S Regulation of transcription by ubiquitination without proteolysis: Cdc34/SCF(Met30)-mediated inactivation of the transcription factor Met4 Cell 2000, 102:303-314. 10.1016/S0092-8674(00)00036-2 10975521
21. Fabrizio P Pletcher SD Minois N Vaupel JW Longo VD Chronological aging-independent replicative life span regulation by Msn2/Msn4 and Sod2 in Saccharomyces cerevisiae FEBS Lett 2004, 557:136-142. 10.1016/ S0014-5793(03)01462-5 14741356
22. Fabrizio P Pozza F Pletcher S Gendron CM Longo VD Regulation of longevity and stress resistance by Sch9 in yeast Science 2001, 292:288-290. 10.1126/science.1059497 11292860
23. Hughes JD Estep PW Tavazoie S Church GM Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae J Mol Biol 2000, 296:1205-1214. 10.1006/jmbi.2000.3519 10698627
24. Beer MA Tavazoie S Predicting gene expression from sequence Cell 2004, 117:185-198. 10.1016/S0092-8674(04)00304-6 15084257
25. Roosen J Engelen K Marchal K Mathys J Griffioen G Cameroni E Thevelein JM De Virgilio C De Moor B Winderickx J PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability Mol Microbiol 2005, 55:862-880. 10.1111/j.1365-2958.2004.04429.x 15661010
26. Gorner W Durchschlag E Martinez-Pastor MT Estruch F Ammerer G amilton B Ruis H Schuller C Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity Genes Dev 1998, 12:586-597. 316529 9472026
27. Pedruzzi I Burckert N Egger P De Virgilio C Saccharomyces cerevisiae Ras/ cAMP pathway controls post-diauxic shift element-dependent transcription through the zinc finger protein Gis1 EMBO J 2000, 19:2569-2579. 212766 10835355 10.1093/emboj/19.11.2569
28. Pedruzzi I Dubouloz F Cameroni E Wanke V Roosen J Winderickx J De Virgilio C TOR and PKA signaling pathways converge on the protein kinase Rim15 to control entry into G0 Mol Cell 2003, 12:1607-1613. 10.1016/ S1097-2765(03)00485-4 14690612
29. Cheng C Fabrizio P Ge H Longo V Li L Inference of transcription modification in long-lived yeast strains from their expression profiles BMC Genomics 2007, 8:219. 1949827 17617911 10.1186/1471-2164-8-219
30. Bhattacharjee A Richards WG Staunton J Li C Monti S Vasa P Ladd C Beheshti J Bueno R Gillette M Loda M Weber G Mark EJ Lander ES Wong W Johnson BE Golub TR Sugarbaker DJ Meyerson M Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proc Natl Acad Sci USA 2001, 98:13790-13795. 61120 11707567 10.1073/pnas.191502998
31. Kel AE Gossling E Reuter I Cheremushkin E Kel-Margoulis OV Liebich I Meinhardt T Reuter I Schacherer F Wingender E MATCH: A tool for searching transcription factor binding sites in DNA sequences Nucleic Acids Res 2003, 31:3576-3579. 169193 12824369 10.1093/nar/gkg585
32. Heinemeyer T Chen X Karas H Kel AE Kel OV Liebich I Meinhardt T Reuter I Schacherer F Wingender E Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms Nucleic Acids Res 1999, 27:318-322. 148171 9847216 10.1093/nar/27.1.318
33. Muller H Helin K The E2F transcription factors: Key regulators of cell proliferation Biochim Biophys Acta 2000, 1470:M1-12. 10656985
34. DeGregori J Johnson DG Distinct and Overlapping Roles for E2F Family Members in Transcription, Proliferation and Apoptosis Curr Mol Med 2006, 6:739-748. 17100600
35. Macleod K pRb and E2f-1 in mouse development and tumorigenesis Curr Opin Genet Dev 1999, 9:31-39. 10.1016/S0959-437X(99)80005-7 10072353
36. Nevins JR The Rb/E2F pathway and cancer Hum Mol Genet 2001, 10:699-703. 10.1093/hmg/10.7.699 11257102
37. Fingerman IM Briggs SD p53-mediated transcriptional activation: From test tube to cell Cell 2004, 117:690-691. 10.1016/j.cell.2004.05.021 15186770
38. Levine AJ Momand J Finlay CA The p53 tumour suppressor gene Nature 1991, 351:453-456. 10.1038/351453a0 2046748
39. Hollstein M Sidransky D Vogelstein B Harris CC p53 mutations in human cancers Science 1991, 253:49-53. 10.1126/science.1905840 1905840
40. Li Q Verma IM NF-kappaB regulation in the immune system Nat Rev Immunol 2002, 2:725-734. 10.1038/nri910 12360211
41. Gilmore TD Introduction to NF-kappaB: Players, pathways, perspectives Oncogene 2006, 25:6680-6684. 10.1038/sj.onc.1209954 17072321
42. Sanceau J Boyd DD Seiki M Bauvois B Interferons inhibit tumor necrosis factor-alpha-mediated matrix metalloproteinase-9 activation via interferon regulatory factor-1 binding competition with NF-kappa B J Biol Chem 2002, 277:35766-35775. 10.1074/jbc.M202959200 12105194
43. Namiki S Nakamura T Oshima S Yamazaki M Sekine Y Tsuchiya K Okamoto R Kanai T Watanabe M IRF-1 mediates upregulation of LMP7 by IFN-gamma and concerted expression of immunosubunits of the proteasome FEBS Lett 2005, 579:2781-2787. 10.1016/j.febslet.2005.04.012 15907481
44. Bouker KB Skaar TC Riggins R Harburger DS Fernandez DR Zwart A Wang A Clarke R Interferon regulatory factor-1 (IRF-1) exhibits tumor suppressor activities in breast cancer associated with caspase activation and induction of apoptosis Carcinogenesis 2005, 26:1527-1535. 10.1093/carcin/bgi113 15878912
45. Rayet B Gelinas C Aberrant rel/nfkb genes and activity in human cancer Oncogene 1999, 18:6938-6947. 10.1038/sj.onc.1203221 10602468
46. Preisler HD Perambakam S Li B Hsu WT Venugopal P Creech S Sivaraman S Tanaka N Alterations in IRF1/IRF2 expression in acute myelogenous leukemia Am J Hematol 2001, 68:23-31. 10.1002/ajh.1144 11559933
47. Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES Mesirov JP Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci USA 2005, 102:15545-15550. 1239896 16199517 10.1073/pnas.0506580102
48. Storey JD Tibshirani R Statistical significance for genomewide studies Proc Natl Acad Sci USA 2003, 100:9440-9445. 170937 12883005 10.1073/ pnas.1530509100