Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites

Vinsensius B Vega^*¹^,2 , Chin-Yo Lin^*¹^,3^,4 , Koon Siew Lai¹ , Say Li Kong¹^,3 , Min Xie¹^,3 , Xiaodi Su⁵ , Huey Fang Teh⁵ , Jane S Thomsen¹ , Ai Li Yeo¹^,3 , Wing Kin Sung² , Guillaume Bourque² and Edison T Liu¹

¹Estrogen Receptor Biology Program, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672

²Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672

³Microarray and Expression Genomics Laboratory, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672

⁴Department of Microbiology and Molecular Biology, Brigham Young University, 753 WIDB, Provo, UT 84602, USA

⁵Institute of Materials Research and Engineering, 3, Research Link, Republic of Singapore 117602

author email corresponding author email* Contributed equally

Genome Biology 2006, 7:R82doi:10.1186/gb-2006-7-9-r82


Published:	9 September 2006

Subject areas: Genome studies, Molecular biology

Additional files

Additional data file 1:

The motif width (window size), size of the flanking regions, and the Laplacian pseudocount (L) were varied. Two sets of sequences were used: (A) with the core ERE intact, and (B) without the core ERE. Overall, single nucleotides appeared to hold certain discriminative power for separating ER binding from ER non-binding sequences.

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Additional data file 2:

Sequence logos for: (A) the 45 binders, after entropy optimization, with 3 bp flanking sequences, shown with its reverse complement, and (B) 116 non-binder sites, obtained from taking the both strands of 58 non-binding loci.

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Additional data file 3:

Monte Carlo P values for the information entropy significance of each base pair location immediately flanking the core ERE.

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