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Computational and Mathematical Methods in Medicine
Volume 2012, Article ID 568950, 10 pages
Research Article

Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

1Department of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
2School of Life science and Technology, Tongji University, Shanghai 200092, China
3Center for Systems Biology, Soochow University, Suzhou Jiangsu 215006, China
4Department of Cardiothoracic Surgery, Second Affiliated Hospital of Soochow University, Suzhou Jiangsu 215004, China

Received 1 November 2012; Accepted 18 December 2012

Academic Editor: Hong-Bin Shen

Copyright © 2012 Min Ding et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Additional file 1 shows the differentially expressed genes in the vicinity of ER binding sites. Using 3 gene expression studies and a criterion of q-value <0.01, we identified 5692 and 6101 up- and down-regulated down-regulated genes between ER+ and ER- breast tumors. Among these genes, 289 up-regulated and 198 down-regulated genes located near the ER binding sites. The details of these 489 estrogen response elements were listed here. Additional file 2 shows the SNPs occurred in the ER-regulated genes located near the binding sites. These SNPs were identified by using the table SNP (131) (dbSNP build 131) in UCSC ( Totally, 836 SNPs in or near 157 ER-regulated genes were identified.

  1. Supplementary Material