Miller JA, Widom J: Collaborative competition mechanism for gene activation in vivo. Mol Cell Biol. 2003, 23: 1623-1632. 10.1128/MCB.23.5.1623-1632.2003.
Article
PubMed
CAS
PubMed Central
Google Scholar
Remenyi A, Scholer HR, Wilmanns M: Combinatorial control of gene expression. Nat Struct Mol Biol. 2004, 11: 812-815. 10.1038/nsmb820.
Article
PubMed
CAS
Google Scholar
Chen L, Glover JN, Hogan PG, Rao A, Harrison SC: Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA. Nature. 1998, 392: 42-48. 10.1038/32100.
Article
PubMed
CAS
Google Scholar
Tan S, Richmond TJ: Eukaryotic transcription factors. Curr Opin Struct Biol. 1998, 8: 41-48. 10.1016/S0959-440X(98)80008-0.
Article
PubMed
CAS
Google Scholar
Davidson EH: Genomic regulatory systems: development and evolution. 2001, San Diego, CA, USA: Academic
Google Scholar
Nagamine N, Kawada Y, Sakakibara Y: Identifying cooperative transcriptional regulations using protein-protein interactions. Nucleic Acids Res. 2005, 33: 4828-4837. 10.1093/nar/gki793.
Article
PubMed
CAS
PubMed Central
Google Scholar
Banerjee N, Zhang MQ: Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res. 2003, 31: 7024-7031. 10.1093/nar/gkg894.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chang YH, Wang YC, Chen BS: Identification of transcription factor cooperativity via stochastic system model. Bioinformatics. 2006, 22: 2276-2282. 10.1093/bioinformatics/btl380.
Article
PubMed
CAS
Google Scholar
Tsai HK, Lu HH, Li WH: Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci USA. 2005, 102: 13532-13537. 10.1073/pnas.0505874102.
Article
PubMed
CAS
PubMed Central
Google Scholar
Aguilar D, Oliva B: Topological comparison of methods for predicting transcriptional cooperativity in yeast. BMC Genomics. 2008, 9: 137-10.1186/1471-2164-9-137.
Article
PubMed
PubMed Central
Google Scholar
Yu H, Gerstein M: Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A. 2006, 103: 14724-14731. 10.1073/pnas.0508637103.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jovelin R, Phillips PC: Evolutionary rates and centrality in the yeast gene regulatory network. Genome Biol. 2009, 10: R35-10.1186/gb-2009-10-4-r35.
Article
PubMed
PubMed Central
Google Scholar
Goh C, Bogan A, Joachimiak M, Walther D, Cohen F: Co-evolution of proteins with their interaction partners. J Mol Biol. 2000, 299: 283-293. 10.1006/jmbi.2000.3732.
Article
PubMed
CAS
Google Scholar
Koretke K, Lupas A, Warren P, Rosenberg M, Brown J: Evolution of two-component signal transduction. Mol Biol Evol. 2000, 17: 1956-1970. 10.1093/oxfordjournals.molbev.a026297.
Article
PubMed
CAS
Google Scholar
Amorim MJ, Cotobal C, Duncan C, Mata J: Global coordination of transcriptional control and mRNA decay during cellular differentiation. Mol Syst Biol. 2010, 6: 380-
Article
PubMed
PubMed Central
Google Scholar
Pál C, Papp B, Hurst LD: Highly expressed genes in yeast evolve slowly. Genetics. 2001, 158: 927-931.
PubMed
PubMed Central
Google Scholar
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH: Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A. 2005, 102: 14338-14343. 10.1073/pnas.0504070102.
Article
PubMed
CAS
PubMed Central
Google Scholar
Beyer A, Workman C, Hollunder J, Radke D, Moller U, Wilhelm T, Ideker T: Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol. 2006, 2: e70-10.1371/journal.pcbi.0020070.
Article
PubMed
PubMed Central
Google Scholar
Bhardwaj N, Kim PM, Gerstein M: Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators. Sci Signal. 2010, 3: ra79-10.1126/scisignal.2001014.
Article
PubMed
Google Scholar
DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997, 278: 680-686. 10.1126/science.278.5338.680.
Article
PubMed
CAS
Google Scholar
Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW: A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell. 1998, 2: 65-73. 10.1016/S1097-2765(00)80114-8.
Article
PubMed
CAS
Google Scholar
Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I: The transcriptional program of sporulation in budding yeast. Science. 1998, 282: 699-705.
Article
PubMed
CAS
Google Scholar
Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA: Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell. 2001, 12: 323-337.
Article
PubMed
CAS
PubMed Central
Google Scholar
Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA: Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998, 95: 717-728. 10.1016/S0092-8674(00)81641-4.
Article
PubMed
CAS
Google Scholar
Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ: Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. PLoS One. 2008, 3: e3112-10.1371/journal.pone.0003112.
Article
PubMed
PubMed Central
Google Scholar
Quackenbush J: Computational analysis of microarray data. Nat Rev Genet. 2001, 2: 418-427. 10.1038/35076576. Review
Article
PubMed
CAS
Google Scholar
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME: Global variation in copy number in the human genome. Nature. 2006, 444: 444-454. 10.1038/nature05329.
Article
PubMed
CAS
PubMed Central
Google Scholar
Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, Mittmann M, et al: Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999, 285: 901-906. 10.1126/science.285.5429.901.
Article
PubMed
CAS
Google Scholar
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M: The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011, 39: D698-704. 10.1093/nar/gkq1116.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xia Y, Franzosa EA, Gerstein MB: Integrated assessment of genomic correlates of protein evolutionary rate. PLoS Comput Biol. 2009, 5: e1000413-10.1371/journal.pcbi.1000413.
Article
PubMed
PubMed Central
Google Scholar
Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Güldener U, Mannhaupt G, Münsterkötter M, Mewes HW: The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004, 32: 5539-5545. 10.1093/nar/gkh894.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gene Ontology Consortium: The Gene Ontology: enhancements for 2011. Nucleic Acids Res. 2012, 40: D559-D564.
Article
Google Scholar
R Development Core Team: R: A language and environment for statistical computing. 2010, Vienna, Austria: R Foundation for Statistical Computing
Google Scholar