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Items: 1 to 20 of 122


A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1.

Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ.

Genome Res. 2006 Dec;16(12):1585-95. Epub 2006 Oct 19.


Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome.

Bieda M, Xu X, Singer MA, Green R, Farnham PJ.

Genome Res. 2006 May;16(5):595-605. Epub 2006 Apr 10.


Transcriptional regulation of the mouse PNRC2 promoter by the nuclear factor Y (NFY) and E2F1.

Zhou D, Masri S, Ye JJ, Chen S.

Gene. 2005 Nov 21;361:89-100. Epub 2005 Sep 21.


An integrated approach to identifying cis-regulatory modules in the human genome.

Won KJ, Agarwal S, Shen L, Shoemaker R, Ren B, Wang W.

PLoS One. 2009;4(5):e5501. doi: 10.1371/journal.pone.0005501. Epub 2009 May 12.


MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D98-103.


Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray.

Jin VX, Leu YW, Liyanarachchi S, Sun H, Fan M, Nephew KP, Huang TH, Davuluri RV.

Nucleic Acids Res. 2004 Dec 17;32(22):6627-35. Print 2004.


A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members.

Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ.

Genome Res. 2007 Nov;17(11):1550-61. Epub 2007 Oct 1.


Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data.

Gu F, Hsu HK, Hsu PY, Wu J, Ma Y, Parvin J, Huang TH, Jin VX.

BMC Syst Biol. 2010 Dec 17;4:170. doi: 10.1186/1752-0509-4-170.


E2F-HDAC complexes negatively regulate the tumor suppressor gene ARHI in breast cancer.

Lu Z, Luo RZ, Peng H, Huang M, Nishmoto A, Hunt KK, Helin K, Liao WS, Yu Y.

Oncogene. 2006 Jan 12;25(2):230-9.


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.


The Innate Immune Database (IIDB).

Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H.

BMC Immunol. 2008 Mar 5;9:7. doi: 10.1186/1471-2172-9-7.


Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

Kamalakaran S, Radhakrishnan SK, Beck WT.

J Biol Chem. 2005 Jun 3;280(22):21491-7. Epub 2005 Mar 24.


Target gene identification from expression array data by promoter analysis.

Werner T.

Biomol Eng. 2001 Mar;17(3):87-94. Review.


A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.


Using local gene expression similarities to discover regulatory binding site modules.

WilczyƄski B, Hvidsten TR, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K.

BMC Bioinformatics. 2006 Nov 17;7:505.


Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.


Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E.

Gene. 2013 Dec 1;531(2):212-9. doi: 10.1016/j.gene.2013.09.011. Epub 2013 Sep 13.


Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase.

Wells J, Yan PS, Cechvala M, Huang T, Farnham PJ.

Oncogene. 2003 Mar 13;22(10):1445-60.


Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells.

Philippakis AA, Busser BW, Gisselbrecht SS, He FS, Estrada B, Michelson AM, Bulyk ML.

PLoS Comput Biol. 2006 May;2(5):e53. Epub 2006 May 26.


CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.

Hestand MS, van Galen M, Villerius MP, van Ommen GJ, den Dunnen JT, 't Hoen PA.

BMC Bioinformatics. 2008 Nov 26;9:495. doi: 10.1186/1471-2105-9-495.

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