About the Human Stat1 ChIP-seq Peak Database (v1)

Usage note: Filters and cookies
cisRED manages your 'Filter' settings via a browser 'cookie'. You must allow your web browser to accept cookies from cisred.org for your filter settings to take effect.

The cisRED Stat1 ChIP-seq peak database holds ~6K conserved motifs that were discovered in 226 search regions of the human genome (Ensembl v35, NCBI 35, hg17). In this initial release, no discovery p-value threshold of was used. Each search region represents a peak in a result set generated by chromatin immunoprecipication and massively parallel Solexa sequencing. Solexa reads were mapped to hg17, rather than hg18, to facilitate comparing results with ENCODE STAT1 results.

The input sequence sets for motif discovery consisted of regions that were ~600bp in size and centered on the experimentally discovered ChIP-seq peaks, and corresponding regions from other species. Inputs were generated from genome data for 16 vertebrate species from Ensembl and the UCSC multiple sequence alignment of April 2006. A typical input set contained sequence data from 10 vertebrate species. (In addition to searching this database, you can browse a list of all 226 search regions.)

An overview of the pipeline and database is available in an NAR 2006 publication. Manuscripts that describe the methods used to identify conserved genomic elements associated with STAT1 peaks are in preparation.

Direct SQL queries can be run against the database cisred_Hsap_Stat1_ChIP_peaks at db.cisred.org, with the username 'anonymous', and no password.