BindDB: an integrated database and webtool platform for “reverse-ChIP” epigenomic analysis

The high-throughput revolution has brought an unprecedented amount of epigenomic data for embryonic stem cells (ESCs), including genome-wide profiles of chromatin-bound proteins and histone modifications generated by chromatinimmunoprecipitation assays (ChIP-seq). As dataset after dataset of ChIP-seq data is added to the pool, the time is ripe to reverse the viewpoint from being factor-oriented to the perspective of genomic locations in order to offer a comprehensive view of chromatin characteristics and regulatory elements that govern coherent gene groups or chromosomal regions. Previously, we collected over 50 such genome-wide datasets in mouse (mESCs), and, using a bioinformatic pipeline which we developed, were able to identify novel regulators of histone genes (Gokhman et al., 2013), demonstrating the power of this approach. We have now built a dynamic database and webtool platform called BindDB that enables in silico “reverse-ChIP” analyses for widespread use within the stem cell community. BindDB includes a significantly expanded epigenomic database, which comprises a collection of over 450 genome-wide datasets in over 40 ESC and iPSC lines from mouse and human, integrated with a webtool that emulates our analysis pipeline.

Authors: Livyatan I, Aaronson Y, Gokhman D, Ashkenazi R and Meshorer E
Year of publication: 2015
Journal: Cell Stem Cell, LETTER| VOLUME 17, ISSUE 6, P647-648, DECEMBER 03, 2015

Link to publication:


“Working memory”