Abstract
GTRD - Gene Transcription Regulation Database (http://gtrd.biouml.org) - is a database of transcription factor binding sites (TFBSs) identified by ChIPseq experiments for human and mouse. Raw ChIPseq data were obtained from ENCODE and SRA and uniformly processed: (i) reads were aligned using Bowtie2; (ii) ChIP-seq peaks were called using peak callers MACS, SISSRs, GEM and PICS; (iii) peaks for the same factor and peak callers, but different experiment conditions (cell line, treatment, etc.), were merged into clusters; (iv) such clusters for different peak callers were merged into metaclusters that were considered as non-redundant sets of TFBSs. In addition to information on location in genome, the sets contain structured information about cell lines and experimental conditions extracted from descriptions of corresponding ChIP-seq experiments. A web interface to access GTRD was developed using the BioUML platform. It provides: (i) browsing and displaying information; (ii) advanced search possibilities, e.g. search of TFBSs near the specified gene or search of all genes potentially regulated by a specified transcription factor; (iii) integrated genome browser that provides visualization of the GTRD data: read alignments, peaks, clusters, metaclusters and information about gene structures from the Ensembl database and binding sites predicted using position weight matrices from the HOCOMOCO database.
Original language | English |
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Pages (from-to) | D61-D67 |
Number of pages | 7 |
Journal | Nucleic Acids Research |
Volume | 45 |
Issue number | D1 |
DOIs | |
Publication status | Published - 4 Jan 2017 |
Keywords
- Animals
- Binding Sites
- Cell Line
- Databases, Genetic
- Humans
- Immunoprecipitation
- Mice
- Regulatory Elements, Transcriptional
- Sequence Analysis, DNA
- Transcription Factors/metabolism
- PROTEIN-DNA INTERACTIONS
- RESOLUTION
- GENOME
- ARCHIVE
- RECEPTOR GENE