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BioMed Research International
Volume 2013 (2013), Article ID 914971, 7 pages
A Quantitative Analysis of the Impact on Chromatin Accessibility by Histone Modifications and Binding of Transcription Factors in DNase I Hypersensitive Sites
1School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
2Shanghai Center for Bioinformation Technology, 1278 Ke Yuan Road, Shanghai 201203, China
Received 31 July 2013; Accepted 3 September 2013
Academic Editor: Tao Huang
Copyright © 2013 Peng Cui 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.
Online Supporting Information S1. The prediction powers using all features with different sample sizes. In each sample size, we randomly sampled 500 times and modeling according to the procedure discussed in method 2.3 in each sample.
Online Supporting Information S2. The input maximum signal dataset including the maximum signals of Chip-seq and DNase-seq in 5000 DNase I hypersensitive sites.
Online Supporting Information S3. The input average signal dataset including the average signals of Chip-seq and DNase-seq in 5000 DNase I hypersensitive sites.
Online Supporting Information S4. The prediction powers (R) using only one feature.
Online Supporting Information S5. The prediction powers (R) using all possible two-feature combinations.
Online Supporting Information S6. The prediction powers (R) using all possible three-feature combinations.
Online Supporting Information S7. The related R codes are available.