Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM: A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 2009, 10: 252-263. 10.1038/nrg2538.
Article
PubMed
CAS
Google Scholar
Margolin AA, Califano A: Theory and limitations of genetic network inference from microarray data. Ann NY Acad Sci. 2007, 1115: 51-72. 10.1196/annals.1407.019.
Article
PubMed
CAS
Google Scholar
He F, Balling R, Zeng A-P: Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives. J Biotechnol. 2009, 144: 190-203. 10.1016/j.jbiotec.2009.07.013.
Article
PubMed
CAS
Google Scholar
Park PJ: ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009, 10: 669-680. 10.1038/nrg2641.
Article
PubMed
CAS
PubMed Central
Google Scholar
Collas P: The current state of chromatin immunoprecipitation. Mol Biotechnol. 2010, 45: 87-100. 10.1007/s12033-009-9239-8.
Article
PubMed
CAS
Google Scholar
Arda HE, Walhout AJ: Gene-centered regulatory networks. Brief Funct Genomics. 2009, 9: 4-12. 10.1093/bfgp/elp049.
Article
PubMed
PubMed Central
Google Scholar
Walhout AJM: Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res. 2006, 16: 1445-1454. 10.1101/gr.5321506.
Article
PubMed
CAS
Google Scholar
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: 166-176. 10.1038/ng1165.
Article
PubMed
CAS
Google Scholar
Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A: Reverse engineering of regulatory networks in human B cells. Nat Genet. 2005, 37: 382-390. 10.1038/ng1532.
Article
PubMed
CAS
Google Scholar
Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A: Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 2009, 326: 257-263. 10.1126/science.1179050.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
Oh SW, Mukhopadhyay A, Dixit BL, Raha T, Green MR, Tissenbaum HA: Identification of direct targets of DAF-16 controlling longevity, metabolism and diapause by chromatin immunoprecipitation. Nat Genet. 2006, 38: 251-257. 10.1038/ng0406-398.
Article
PubMed
Google Scholar
Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK, Fraenkel E, Bell GI, Young RA: Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol. 2006, 2: 10.1038/msb4100059. 2006.0017
Google Scholar
Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M: Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev. 2007, 21: 385-390. 10.1101/gad.1509607.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE: Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature. 2009, 462: 65-70. 10.1038/nature08531.
Article
PubMed
CAS
Google Scholar
Tsukagoshi H, Busch W, Benfey PN: Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root. Cell. 2010, 143: 606-616. 10.1016/j.cell.2010.10.020.
Article
PubMed
CAS
Google Scholar
Deplancke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Reece-Hoyes JS, Hope IA, Tissenbaum HA, Mango SE, Walhout AJ: A gene-centered C. elegans protein-DNA interaction network. Cell. 2006, 125: 1193-1205. 10.1016/j.cell.2006.04.038.
Article
PubMed
CAS
Google Scholar
Vermeirssen V, Barrasa MI, Hidalgo C, Babon JAB, Sequerra R, Doucette-Stam L, Barabasi AL, Walhout AJM: Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res. 2007, 17: 1061-1071. 10.1101/gr.6148107.
Article
PubMed
CAS
PubMed Central
Google Scholar
Martinez NJ, Ow MC, Barrasa MI, Hammell M, Sequerra R, Doucette-Stamm L, Roth FP, Ambros V, Walhout AJM: A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev. 2008, 22: 2535-2549. 10.1101/gad.1678608.
Article
PubMed
CAS
PubMed Central
Google Scholar
Arda HE, Taubert S, Conine C, Tsuda B, Van Gilst MR, Sequerra R, Doucette-Stam L, Yamamoto KR, Walhout AJM: Functional modularity of nuclear hormone receptors in a C. elegans gene regulatory network. Mol Syst Biol. 2010, 6: 367-10.1038/msb.2010.23.
Article
PubMed
PubMed Central
Google Scholar
Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN: A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol. 2011, 7: 459-10.1038/msb.2010.114.
Article
PubMed
PubMed Central
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS: Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9: R137-10.1186/gb-2008-9-9-r137.
Article
PubMed
PubMed Central
Google Scholar
Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Brent MR, Walhout AJ: Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat Methods. 2007, 4: 659-664. 10.1038/nmeth1063.
Article
PubMed
CAS
Google Scholar
Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, Moore T, Hudson JR, Hartley JL, Brasch MA, Vandenhaute J, Boulton S, Endress GA, Jenna S, Chevet E, Papasotiropoulos V, Tolias PP, Ptacek J, Snyder M, Huang R, Chance MR, Lee H, Doucette-Stamm L, Hill DE, Vidal M: C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet. 2003, 34: 35-41. 10.1038/ng1140.
Article
PubMed
Google Scholar
Rual JF, Hirozane-Kishikawa T, Hao T, Bertin N, Li S, Dricot A, Li N, Rosenberg J, Lamesch P, Vidalain PO, Clingingsmith TR, Hartley JL, Esposito D, Cheo D, Moore T, Simmons B, Sequerra R, Bosak S, Doucette-Stamm L, Le Peuch C, Vandenhaute J, Cusick ME, Albala JS, Hill DE, Vidal M: Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res. 2004, 14: 2128-2135. 10.1101/gr.2973604.
Article
PubMed
CAS
PubMed Central
Google Scholar
Deplancke B, Vermeirssen V, Arda HE, Martinez NJ, Walhout AJ: Gateway-compatible yeast one-hybrid screens. Cold Spring Harb Protoc. 2006, 14: 2093-2101. 10.1101/pdb.prot4590.
Google Scholar
Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EE: A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev. 2007, 21: 436-449. 10.1101/gad.1509007.
Article
PubMed
CAS
PubMed Central
Google Scholar
Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z: Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res. 2004, 32: 1372-1381. 10.1093/nar/gkh299.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bailey TL, Williams N, Misleh C, Li WW: MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006, 34: W369-W373. 10.1093/nar/gkl198.
Article
PubMed
CAS
PubMed Central
Google Scholar
Stormo GD: Motif discovery using expectation maximization and Gibbs' sampling. Methods Mol Biol. 2010, 674: 85-95. full_text.
Article
PubMed
CAS
Google Scholar
Newburger DE, Bulyk ML: UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res. 2009, 37: D77-D82. 10.1093/nar/gkn660.
Article
PubMed
CAS
PubMed Central
Google Scholar
Grove CA, deMasi F, Barrasa MI, Newburger D, Alkema MJ, Bulyk ML, Walhout AJ: A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell. 2009, 138: 314-327. 10.1016/j.cell.2009.04.058.
Article
PubMed
CAS
PubMed Central
Google Scholar
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML: Diversity and complexity in DNA recognition by transcription factors. Science. 2009, 324: 1720-1723. 10.1126/science.1162327.
Article
PubMed
CAS
PubMed Central
Google Scholar
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006, 34: D108-D110. 10.1093/nar/gkj143.
Article
PubMed
CAS
PubMed Central
Google Scholar
Reece-Hoyes JS, Deplancke B, Barrasa MI, Hatzold J, Smit RB, Arda HE, Pope PA, Gaudet J, Conradt B, Walhout AJ: The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res. 2009, 37: 3689-3698. 10.1093/nar/gkp232.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ow MC, Martinez NJ, Olsen P, Silverman S, Barrasa MI, Conradt B, Walhout AJM, Ambros VR: The FLYWCH transcription factors FLH-1, FLH-2 and FLH-3 repress embryonic expression of microRNA genes in C. elegans. Genes Dev. 2008, 22: 2520-2534. 10.1101/gad.1678808.
Article
PubMed
CAS
PubMed Central
Google Scholar
Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, Ahringer J, Li H, Kenyon C: Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature. 2003, 424: 277-283. 10.1038/nature01789.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M: KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010, 38: D355-360. 10.1093/nar/gkp896.
Article
PubMed
CAS
PubMed Central
Google Scholar
Timmons L, Court DL, Fire A: Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene. 2001, 263: 103-112. 10.1016/S0378-1119(00)00579-5.
Article
PubMed
CAS
Google Scholar
Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, Welchman DP, Zipperlen P, Ahringer J: Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003, 421: 231-237. 10.1038/nature01278.
Article
PubMed
CAS
Google Scholar
Reece-Hoyes JS, Shingles J, Dupuy D, Grove CA, Walhout AJ, Vidal M, Hope IA: Insight into transcription factor gene duplication from Caenorhabditis elegans promoterome-driven expression patterns. BMC Genomics. 2007, 8: 27-10.1186/1471-2164-8-27.
Article
PubMed
PubMed Central
Google Scholar
Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, et al: An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 2010, 140: 744-752. 10.1016/j.cell.2010.01.044.
Article
PubMed
CAS
Google Scholar
Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD: Transcription factors bind thousands of active an inactive regions in the Drosophila blastoderm. PLoS Biol. 2008, 6: e27-10.1371/journal.pbio.0060027.
Article
PubMed
PubMed Central
Google Scholar
Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ: Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell. 2010, 18: 662-674. 10.1016/j.devcel.2010.02.014.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hollenhorst PC, Shah AA, Hopkins C, Graves BJ: Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev. 2007, 21: 1882-1894. 10.1101/gad.1561707.
Article
PubMed
CAS
PubMed Central
Google Scholar
MacNeil L, Walhout AJM: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res. 2011, 10.1101/gr.097378.109.
Google Scholar
Dekker J: Gene regulation in the third dimension. Science. 2008, 319: 1793-1794. 10.1126/science.1152850.
Article
PubMed
CAS
PubMed Central
Google Scholar
Dekker J, Rippe K, Dekker M, Kleckner N: Capturing chromosome conformation. Science. 2002, 295: 1306-1311. 10.1126/science.1067799.
Article
PubMed
CAS
Google Scholar