Research
Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites
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* Corresponding authors: Vinsensius B Vega vegav@gis.a-star.edu.sg - Edison T Liu liue@gis.a-star.edu.sg
- † Equal contributors
1 Estrogen Receptor Biology Program, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672
2 Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672
3 Microarray and Expression Genomics Laboratory, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672
4 Department of Microbiology and Molecular Biology, Brigham Young University, 753 WIDB, Provo, UT 84602, USA
5 Institute of Materials Research and Engineering, 3, Research Link, Republic of Singapore 117602
Genome Biology 2006, 7:R82 doi:10.1186/gb-2006-7-9-r82
Published: 9 September 2006Additional 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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