Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

Abstract

The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and DNA methylation patterns. The ENCODE project generates data utilizing a variety of techniques that can enrich for regulatory regions, such as chromatin immunoprecipitation (ChIP), micrococcal nuclease (MNase) digestion and DNase I digestion, followed by deeply sequencing the resulting DNA. As part of the ENCODE project, we have developed a Web-accessible repository accessible at http://factorbook.org. In Wiki format, factorbook is a transcription factor (TF)-centric repository of all ENCODE ChIP-seq datasets on TF-binding regions, as well as the rich analysis results of these data. In the first release, factorbook contains 457 ChIP-seq datasets on 119 TFs in a number of human cell lines, the average profiles of histone modifications and nucleosome positioning around the TF-binding regions, sequence motifs enriched in the regions and the distance and orientation preferences between motif sites.

Figure 1.

The matrix on the factorbook home page. The user can click on a specific TF and go directly to its page, or specify a protein family to display its TF members. Each number in the matrix represents the number of ChIP-seq experiments (and resultant ENCODE datasets) performed for that factor in a given cell line.

Figure 2.

Average profiles of modified histones around the summit of ChIP-seq peaks. Profiles are shown for the [−2 kb, +2 kb] window around the summits of TF ChIP-seq peaks, with proximal peaks shown as dashed lines and distal peaks shown as solid lines. The graphs are designed in an interactive fashion to allow the user to select data for a specific histone modification.

Figure 3.

Average profiles of nucleosomes around the summit of ChIP-seq peaks. Average nucleosome positioning profiles are shown for the [−2 kb, +2 kb] window around the summits of TF ChIP-seq peaks. Red lines represent proximal peaks and blue lines show distal peaks.

Figure 4.

Motifs enriched in the top 500 ChIP-seq peaks of CTCF. This section displays five motifs (M1–M5), with motif name and sequence logo as well as the number of peaks out of the top 500 ChIP-seq peaks containing a motif site. The user can customize the motifs shown by cell line, laboratory, protocol, treatment and antibody.

Figure 5.

Heatmaps of TF-binding profiles and histone modification profiles around c-Fos peaks. Binding strengths of TFs and enrichment of histone marks are represented in a normalized scale. Rows indicate the ChIP-seq peaks of the pivoting TF (in this case c-Fos) and are inversely ordered by the ChIP signals of c-Fos peaks. TF-binding profiles are shown over a span of 2 kb while histone marks are shown over a span of 10 kb. Heatmaps for each TF are specific to the dataset and cell line of the pivoting TF.