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This article is to share with you about the use of GTRD databases. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

GTRD collects transcription factor-related chip_seq data from SRA, GEO, ENCODE and other public databases, uses the standard process for peak calling analysis, and predicts the transcription factor binding site TFBS based on the existing transcription factor motif data. The database is located at

Http://gtrd.biouml.org/

The pipeline for the entire database construction is as follows

The reads was compared with the genome by bowtie2, and the peak region of the transcription factor was obtained by peak calling using MACS,SISSRS and other four softwares.

For the same transcription factor, if the center distance of two peak intervals is less than 50bp, the peak regions obtained by the same peak caling software will be merged into one interval, which is used to cluster the original peak, that is, cluster.

For the same transcription factor, all the peak regions obtained by a variety of peak calling software are grouped into a group of peak regions whose peak center is smaller than 50bp, and a peak is selected as a representative according to the priority of the software, and each software priority is GEM, PICS, MACS, SISSRs. This clustering method is called MetaClusters, and a non-redundant peak interval of all transcription factors is constructed.

The common usage scenarios of this database are as follows

1. Query the raw data of transcription factor chip_seq

two。 Search for transcription factor binding sites on genes

3. Query the target genes of transcription factors

In addition to online query, the database is also available for download, with the following links

Http://gtrd.biouml.org/downloads/19.04/chip-seq/

GTRD contains the most comprehensive data of transcription factors, and its function of querying the target genes of transcription factors is really very practical.

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