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Open Access Highly Accessed Methodology article

iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets

Yingying Wei1, Xia Li23, Qian-fei Wang2 and Hongkai Ji1*

  • * Corresponding author: Hongkai Ji hji@jhsph.edu

  • † Equal contributors

Author Affiliations

1 Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe StreetBaltimore, Maryland 21205, USA

2 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, P.R. China

3 University of Chinese Academy of Sciences, Beijing 100049, P.R. China

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BMC Genomics 2012, 13:681  doi:10.1186/1471-2164-13-681

Published: 29 November 2012

Additional files

Additional file 1:

Supplemental Methods. A PDF file including: data preprocessing procedures; method of moment estimation in the beta distribution; parameter choice for the Dirichlet prior; derivation of the EM algorithm for iASeq; Bayesian Information Criterion for choosing K; data generation procedure in simulation studies; single dataset based EM analysis.

Format: PDF Size: 77KB Download file

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Additional file 2:

Table S1. Description of all GM12878 ChIP-seq and RNA-seq studies. An excel file showing the name of TF and HM, the number of replicates for each dataset in GM12878 cells.

Format: XLS Size: 42KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Table S2. Raw read count data for 94,519 analyzed SNPs.

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Additional file 4:

Supplemental comparison of defining allele-specific SNPs as SNPs that have RNA-seq exonic ASE SNPs in their 1kb neighborhood. Supplemental Figure 3 — ROC curves for GM12878 using Caltech Exonic RNA-seq ASE SNPs as gold standard. Supplemental Figure 4 — ROC curves for GM12878 using Caltech autosomal exonic RNA-seq ASE SNPs as gold standard. Supplemental Figure 5 — ROC curves for GM12878 using Yale Exonic RNA-seq ASE SNPs as gold standard. Supplemental Figure 6 — ROC curves for GM12878 using Yale autosomal exonic RNA-seq ASE SNPs as gold standard. Supplemental Table 4 — Comparison of iASeq and AlleleSeq using Caltech RNA-seq exonic ASE SNPs as gold standard. Supplemental Table 5 — Comparison of iASeq and AlleleSeq using Yale RNA-seq exonic ASE SNPs as gold standard.

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Additional file 5:

Figure S1. ROC curves for GM12878 using Yale Exonic RNA-seq ASE SNPs as gold standard.

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Additional file 6:

Figure S2. ROC curves for GM12878 using Yale autosomal exonic RNA-seq ASE SNPs as gold standard.

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Additional file 7:

Table S3. Comparison of iASeq and AlleleSeq using Yale RNA-seq exonic ASE SNPs as gold standard.

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Additional file 8:

Figure S7. The ROC curves for comparison between AlleleSeq and iASeq.

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