Mullen AC, Orlando DA, Newman JJ, Loven J, Kumar RM, Bilodeau S, Reddy J, Guenther MG, DeKoter RP, Young RA. Master transcription factors determine cell-type-specific responses to TGF-beta signaling. Cell. 2011;147(3):565–76.
Article
CAS
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, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 2010;140(5):744–52.
Article
CAS
PubMed
Google Scholar
Zhang Z, Chang CW, Goh WL, Sung WK, Cheung E. CENTDIST: discovery of co-associated factors by motif distribution. Nucleic Acids Res. 2011;39(Web Server issue):W391–399.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolberger C. Multiprotein-DNA complexes in transcriptional regulation. Annu Rev Biophys Biomol Struct. 1999;28:29–56.
Article
CAS
PubMed
Google Scholar
Whitington T, Frith MC, Johnson J, Bailey TL. Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Res. 2011;39(15):e98.
Article
CAS
PubMed
PubMed Central
Google Scholar
MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keranen SV, et al. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 2009;10(7):R80.
Article
PubMed
PubMed Central
Google Scholar
Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Hendriks CLL, et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm (vol 6, pg e27, 2008). Plos Biol. 2008;6(7):1600–0.
Chen MJ, Chou LC, Hsieh TT, Lee DD, Liu KW, Yu CY, Oyang YJ, Tsai HK, Chen CY. De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae. Bioinformatics. 2012;28(5):701–8.
Article
CAS
PubMed
Google Scholar
Cheng C, Min R, Gerstein M. TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. Bioinformatics. 2011;27(23):3221–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Diez D, Hutchins AP, Miranda-Saavedra D. Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. Nucleic Acids Res. 2014;42(1):e6.
Article
CAS
PubMed
Google Scholar
Fleming JD, Pavesi G, Benatti P, Imbriano C, Mantovani R, Struhl K. NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res. 2013;23(8):1195–209.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu J, Giannola DM, Zhang Y, Rivera AJ, Emerson SG. NF-Y cooperates with USF1/2 to induce the hematopoietic expression of HOXB4. Blood. 2003;102(7):2420–7.
Article
CAS
PubMed
Google Scholar
Gobin SJ, Biesta P, Van den Elsen PJ. Regulation of human beta 2-microglobulin transactivation in hematopoietic cells. Blood. 2003;101(8):3058–64.
Article
CAS
PubMed
Google Scholar
Muckenthaler MU, Rodrigues P, Macedo MG, Minana B, Brennan K, Cardoso EM, Hentze MW, de Sousa M. Molecular analysis of iron overload in beta2-microglobulin-deficient mice. Blood Cells Mol Dis. 2004;33(2):125–31.
Article
CAS
PubMed
Google Scholar
Ouyang Z, Zhou Q, Wong WH. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A. 2009;106(51):21521–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sikora-Wohlfeld W, Ackermann M, Christodoulou EG, Singaravelu K, Beyer A. Assessing computational methods for transcription factor target gene identification based on ChIP-seq data. PLoS Comput Biol. 2013;9(11):e1003342.
Article
PubMed
PubMed Central
Google Scholar
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009;27(1):66–75.
Article
CAS
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, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
Article
PubMed
PubMed Central
Google Scholar
Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008;26(12):1351–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014;42(Database issue):D764–770.
Article
CAS
PubMed
Google Scholar
Jabrane-Ferrat N, Nekrep N, Tosi G, Esserman LJ, Peterlin BM. Major histocompatibility complex class II transcriptional platform: assembly of nuclear factor Y and regulatory factor X (RFX) on DNA requires RFX5 dimers. Mol Cell Biol. 2002;22(15):5616–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dooley KA, Millinder S, Osborne TF. Sterol regulation of 3-hydroxy-3-methylglutaryl-coenzyme A synthase gene through a direct interaction between sterol regulatory element binding protein and the trimeric CCAAT-binding factor/nuclear factor Y. J Biol Chem. 1998;273(3):1349–56.
Article
CAS
PubMed
Google Scholar
Lee LC, Chen CM, Wang HC, Hsieh HH, Chiu IS, Su MT, Hsieh-Li HM, Wu CH, Lee GC, Lee-Chen GJ, et al. Role of the CCAAT-binding protein NFY in SCA17 pathogenesis. PLoS One. 2012;7(4):e35302.
Article
CAS
PubMed
PubMed Central
Google Scholar
Panne D, Maniatis T, Harrison SC. An atomic model of the interferon-beta enhanceosome. Cell. 2007;129(6):1111–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B. Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res. 2015;43(4):e27.
Article
PubMed
Google Scholar
Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202–208.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu CC, Lin CC, Chen WS, Chen HY, Chang PC, Chen JJ, Yang PC. CRSD: a comprehensive web server for composite regulatory signature discovery. Nucleic Acids Res. 2006;34(Web Server issue):W571–577.
Article
CAS
PubMed
PubMed Central
Google Scholar
An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489(7414):57-74.
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010;38(Database issue):D105–110.
Article
CAS
PubMed
Google Scholar
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2014, 42(Database issue):D7-17.
Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell. 2007;130(1):77–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genet. 2013;9(8):e1003571.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yuan A, Hsiao YJ, Chen HY, Chen HW, Ho CC, Chen YY, Liu YC, Hong TH, Yu SL, Chen JJ, et al. Opposite Effects of M1 and M2 Macrophage Subtypes on Lung Cancer Progression. Sci Rep. 2015;5:14273.
Article
CAS
PubMed
PubMed Central
Google Scholar
Su TJ, Ku WH, Chen HY, Hsu YC, Hong QS, Chang GC, Yu SL, Chen JJ. Oncogenic miR-137 contributes to cisplatin resistance via repressing CASP3 in lung adenocarcinoma. Am J Cancer Res. 2016;6(6):1317–30.
PubMed
PubMed Central
Google Scholar