The raw data can be found here http://krishna.gs.washington.edu/martin/download/cadd_training/. The real SNV, insertion and deletion samples sum up to 16,627,775. We randomly sample equal number of simutation samples (SNV, insertion and deletion), combine with the real data, and get a dataset of 33,255,550 samples.

This dataset is transormed into svmlight format with script impute2svmlight.py, which is provided by Dr. Martin Kircher (the author of CADD paper). Note that to do this, the python package svmlight-loader is needed

tree-hmm sample data from the ENCODE human project http://cbcl.ics.uci.edu/public_data/tree-hmm-sample-data

Our ChIP-seq analysis of LRH-1 can be found at: http://cbcl.ics.uci.edu/public_data/LRH-1

http://cbcl.ics.uci.edu/public_data/FXR/

ChipSeq was performed on SREBP-2 and peaks were called using GLITR. We also re-analyzed SREBP-1 using GLITR. Supplemental Tables, Figures, and datasets are available: SREBP2

Included here is ChIP-Seq raw and processed data from:

Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. PNAS 2009 106:13765-13769; Young-Kyo Seo, Hansook Kim Chong, Aniello M. Infante, Seung-Soon Im, Xiaohui Xie, and Timothy F. Osborne

• Raw sequence data (raw_data/*_sequence.txt) was processed using eland to create raw/*_eland_multi.txt
• ChipSeq-mini 2.0 (http://woldlab.caltech.edu/html/software, now part of the ERANGE package) was used to process the eland files and produce the processed/*.bed files.
• IgG files are for the control run, SREBP1 files are after fasting and refeeding. See paper for details.

1. Processed Data
2. Raw Data