Difference between revisions of "GTRD"

Revision as of 13:10, 23 October 2018

Gene Transcription Regulation Database (GTRD) is a database of transcription factor (TF) binding sites identified from ChIP-seq experiments that were systematically collected and uniformly processed using a special workflow (pipeline) for a BioUML platform (http://www.biouml.org). Raw ChIP-seq data and experiment information were collected from:

• literature
• GEO
• SRA
• ENCODE.

Initial ChIP-seq and DNase-seq raw data were uniformly processed using specially developed workflow (pipeline) for the BioUML platform. ChIP-seq processing pipeline included the following steps:

• sequenced reads were aligned to the corresponding reference genome using Bowtie2;
• peaks were identified using MACS, SISSR, GEM and PICS peak callers;
• peaks computed for the same TF and peak calling method, but different experiment conditions (e.g., cell line, treatment, etc.) were joined into clusters;
• clusters for the same TF revealed by different peak calling methods were joined into metaclusters.

DNase-seq processing pipeline included the following steps:

• sequenced reads were aligned to the corresponding reference genome using Bowtie2;
• regions of open chromatin were identified using MACS2 and Hotspot2;
• de novo putative protein-DNA interactions were revealed using a digital genomic footprinting tool Wellington.

Learn more about GTRD build process

GTRD database is freely available for non-commercial organizations.

Database statistics (18.06 version)

ChIP-seq experiments by species

Control experiments

General statistics:

Transription factors by species

Ten most studied TFs are listed bellow:

DNase-seq experiments by species

Database structure

The metadata concerning GTRD is stored in MySQL tables.

Each ChIP-seq and DNase-seq experiment has a row in 'chip_experiments' or 'dnase-experiments' table, respectively, which assigns id and stores basic information about experiment. 'chip_experiments' table has the following structure:

'dnase_experiments' table has the following structure:

The links to external databases stored in 'external_refs' table:

GTRD uses the following object identifiers:

The relationship between these objects is provided by a 'hub' table:

ChIP-seq and DNase-seq reads, alignments and peaks links to experiments with hub table in the following way:

Web interface

Web interface to GTRD is available here. It provides capabilities for searching and browsing GTRD.

Start page

Start page contains search boxes and the links to browse all experiments in the repository tree, documentation, help (wiki pages) and transcription factor classification tree.

Search capabilities

Search GTRD

Open ChIP-seq peaks

The ChIP-seq experiments contained in GTRD can be queried from the search box on the Start page. GTRD uses Lucene engine for indexing and quering ChIP-seq experiments that provides rich syntax for searching. The search can be performed by transcription factor(name or uniprot ID), cell line, antibody or treatment/conditions.

For example, to search for STAT transcription factors enter stat* in the search field and press enter. You can restrict query to HeLa cells treated with interferon with following query:

 tfTitle:stat* AND cell:hela AND treatment:IFN

The list of matching ChIP-seq experiments will appear in the 'Search result' tab. Select one of them to view detailed ChIP-seq experiment information in the information box. The information box also provides links to the experiment data: reads, alignments and peaks.

To view peaks or alignments click the link in the ChIP-seq experiment information box, the track will be opened as table. The track can be exported by pressing 'Export' button or opened in the genome browser by pressing 'Open as track' button in the general control panel.

Repository structure

GTRD is organized in hierarchical Repository.

The GTRD/Data folder contains following items:

• DNase experiments - DNase-seq experiments metainformation
• alignments - ChIP-seq read alignments
• clusters - ChIP-seq-derived meta-clusters
• experiments - ChIP-seq experiments metainformation
• peaks - ChIP-seq and DNase-seq peaks identified by peak callers

GTRD/Dictionaries/classification is TFClass classification tree used by GTRD to reference transcription factors. GTRD/Dictionaries/cells is a collection of cells and tissues used by GTRD