Research article
Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq
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* Corresponding author: X Shirley Liu xsliu@jimmy.harvard.edu
- † Equal contributors
1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, 44 Binney St, Boston, MA 02115, USA
2 Simons Center for Systems Biology, Institute for Advanced Study, Einstein Dr, Princeton, NJ 08540, USA
BMC Genomics 2008, 9:537 doi:10.1186/1471-2164-9-537
Published: 13 November 2008Additional files
Additional file 1:
Supplementary materials. This file includes seven supplementary figures and two supplementary tables: Figure S1. Nucleosome positioning signal after extending each tag to 150 nt in the 3' direction and taking the middle 75 nt (A), 45 nt (B), and 25 nt (C). Figure S2. Genomic distribution of identified positioned nucleosomes under different p-value cutoff. Figure S3. Percentage of DNase I HS sites of human CD4+ T cell containing identified positioned nucleosomes. Figure S4. Correlation between histone modification profiles at the same nucleosome loci. Figure S5. Co-occurrence of different histone modification pairs on the same positioned nucleosome loci under different cutoffs for histone modification assignment. Figure S6. Enrichment of co-occurrence of histone modification pairs on adjacent positioned nucleosome loci. Figure S7. Poisson-based p-values vs. FDR (q-value). Table S1. The ChIP-Seq tag number, modified nucleosome number, percentage of tags located in modified nucleosomes, ChIP-Seq efficiency and modification type for each histone modification. Table S2. Number and distribution of identified positioned nucleosomes under different p-value cutoff.
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