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

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

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.

Format: DOC Size: 75KB Download file

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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.

Format: DOC Size: 47KB Download file

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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.

Format: DOC Size: 38KB Download file

This file can be viewed with: Microsoft Word Viewer


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