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Items: 1 to 20 of 173


A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells.

Charos AE, Reed BD, Raha D, Szekely AM, Weissman SM, Snyder M.

Genome Res. 2012 Sep;22(9):1668-79. doi: 10.1101/gr.127761.111.


Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.

Genome Res. 2012 Sep;22(9):1798-812. doi: 10.1101/gr.139105.112.


A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.

Heyndrickx KS, Van de Velde J, Wang C, Weigel D, Vandepoele K.

Plant Cell. 2014 Oct;26(10):3894-910. doi: 10.1105/tpc.114.130591. Epub 2014 Oct 31.


Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions.

Van Nostrand EL, Kim SK.

Genome Res. 2013 Jun;23(6):941-53. doi: 10.1101/gr.152876.112. Epub 2013 Mar 26.


Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data.

Goi C, Little P, Xie C.

BMC Genomics. 2013;14 Suppl 5:S2. doi: 10.1186/1471-2164-14-S5-S2. Epub 2013 Oct 16.


The comprehensive transcriptional analysis in Caenorhabditis elegans by integrating ChIP-seq and gene expression data.

He K, Shao J, Zhao Z, Liu D.

Genet Res (Camb). 2014;96:e005. doi: 10.1017/S0016672314000081.


Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.


BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data.

Kähärä J, Lähdesmäki H.

Bioinformatics. 2015 Sep 1;31(17):2852-9. doi: 10.1093/bioinformatics/btv294. Epub 2015 May 7.


Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes.

Sethi I, Sinha S, Buck MJ.

BMC Genomics. 2014 Nov 29;15:1042. doi: 10.1186/1471-2164-15-1042.


ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. doi: 10.1093/nar/gks1060. Epub 2012 Nov 17.


Sequence and chromatin determinants of cell-type-specific transcription factor binding.

Arvey A, Agius P, Noble WS, Leslie C.

Genome Res. 2012 Sep;22(9):1723-34. doi: 10.1101/gr.127712.111.


Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.

Yáñez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A.

Genome Res. 2012 Oct;22(10):2018-30. doi: 10.1101/gr.132811.111. Epub 2012 Apr 25.


Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network.

Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, Ni T, Gamble CE, Gisselbrecht SS, Zhu J, Bulyk ML, Ovcharenko I, Michelson AM.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20768-73. doi: 10.1073/pnas.1210415109. Epub 2012 Nov 26.


De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.

Niu M, Tabari ES, Su Z.

BMC Genomics. 2014 Dec 2;15:1047. doi: 10.1186/1471-2164-15-1047.


DNA sequence variants in PPARGC1A, a gene encoding a coactivator of the ω-3 LCPUFA sensing PPAR-RXR transcription complex, are associated with NV AMD and AMD-associated loci in genes of complement and VEGF signaling pathways.

SanGiovanni JP, Chen J, Sapieha P, Aderman CM, Stahl A, Clemons TE, Chew EY, Smith LE.

PLoS One. 2013;8(1):e53155. doi: 10.1371/journal.pone.0053155. Epub 2013 Jan 15.


Mapping functional transcription factor networks from gene expression data.

Haynes BC, Maier EJ, Kramer MH, Wang PI, Brown H, Brent MR.

Genome Res. 2013 Aug;23(8):1319-28. doi: 10.1101/gr.150904.112. Epub 2013 May 1.


An exonic peroxisome proliferator-activated receptor-γ coactivator-1α variation may mediate the resting energy expenditure through a potential regulatory role on important gene expression in this pathway.

Mirzaei K, Hossein-nezhad A, Emamgholipour S, Ansar H, Khosrofar M, Tootee A, Alatab S.

J Nutrigenet Nutrigenomics. 2012;5(2):59-71. Epub 2012 May 31.


Discovering transcription factor regulatory targets using gene expression and binding data.

Maienschein-Cline M, Zhou J, White KP, Sciammas R, Dinner AR.

Bioinformatics. 2012 Jan 15;28(2):206-13. doi: 10.1093/bioinformatics/btr628. Epub 2011 Nov 13.


Elucidating functional context within microarray data by integrated transcription factor-focused gene-interaction and regulatory network analysis.

Werner T, Dombrowski SM, Zgheib C, Zouein FA, Keen HL, Kurdi M, Booz GW.

Eur Cytokine Netw. 2013 Jun;24(2):75-90. doi: 10.1684/ecn.2013.0336.


Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

Müller-Molina AJ, Schöler HR, Araúzo-Bravo MJ.

PLoS One. 2012;7(11):e49086. doi: 10.1371/journal.pone.0049086. Epub 2012 Nov 28.

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