data

DANN data
tree-hmm sample .bam's from chr19
LRH-1 ChIP-seq Data
FXR ChIP-seq Data
SREBP-2 ChIP-seq Data
SREBP-1 ChIP-seq Data

DANN data

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), and the python package svmlight-loader. We roughly partition the dataset into 80% for training, 10% for validation and 10% for testing. Their svmlight files are here:

tree-hmm sample .bam's from chr19

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

LRH-1 ChIP-seq Data

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

FXR ChIP-seq Data

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

SREBP-2 ChIP-seq Data

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

SREBP-1 ChIP-seq Data

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.