GTRD

v17.04

GTRD
Gene Transcription Regulation Database

The most complete collection of uniformly processed ChIP-seq data to identify transcription factor binding sites for human and mouse. Convenient web interface with advanced search, browsing and genome browser based on the BioUML platform. For support or any questions contact ivan@nulldote.ru

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Workflow
How it was constructed?

ChIP-seq experiment information and raw data were collected from publically available sources. Sequenced reads were aligned using Bowtie2 and ChIP-seq peaks were called using 4 different methods. Peaks were merged into clusters and metaclusters to produce non-redundant set of transcription factor binding sites.

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Statistics
version 17.04

3075 new 8828 ChIP-seq experiments
171 new 713 Transcription factors
51% new 372 107 532 423 ChIP-seq reads
39% new 239 502 628 829 Reads aligned
56% new 659 388 760 ChIP-seq peaks
59% new 419 661 078 Clusters
50% new 60 472 672 Metaclusters

Learn more »

How to cite

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. I.S. Yevshin, R.N. Sharipov, T.F. Valeev, A.E. Kel, F.A. Kolpakov. Nucleic Acids Res. 2017 Jan 4;45(D1):D61-D67.

License

Users may freely use the GTRD database for non-commercial purposes as long as they properly cite it. If you intend to use GTRD for a commercial purpose, please contact ivan@nulldote.ru to arrange a license.

v17.04

GTRD
Gene Transcription Regulation Database

Workflow
How it was constructed?

Statistics
version 17.04

How to cite

License

Studies citing GTRD

User interface

Overview

Start page

Browse ChIP-seq experiments as table

Browse ChIP-seq experiments in TFClass tree

Integrated genome browser

Find TF binding sites near the specified gene

Find genes potentially regulated by the specified TF

Use cases

Search ChIP-seq experiments by transcription factor

Step 1
Enter TF name into the search box and press enter.
Search results will appear in the bottom pane.

Step 2
Click on the experiment to see detailed experiment information in the bottom-left pane.

Step 3
You can use * in the search field for fuzzy matching.
Enter stat* to search for any stat TF.

Browse ChIP-seq peaks in genome browser

Step 1
Select 'Organism' and 'ChIP-seq peak calling method'.
Press 'Show' button.

Step 2
Genome browser will open.
Select additional tracks to open and press OK.

Step 3
Genome browser shows coverage profile for the large number of sites.
Zoom in to see individual sites. Press 'Semantic zoom in' button in the toolbar or use Ctrl+Scroll mouse wheel.

Step 4
Zoom in once more to see TF names

Step 5
Select individual site to see detailed site info in the bottom-left pane.

Step 6
Select the 'Sites' tab in the bottom right pane to view all visible sites in the table.
Or export sites to file using 'Export' button in the toolbar.

Find transcription factor binding sites on gene

Step 1
To search for c-Jun binding sites near the TP53 gene:
enter TP53 into 'Gene symbol' field and select c-Jun transcription factor.
You also can restrict search to specific cell line and treatment.
Press Run button.

Step 2
Genome browser will open.
Select additional tracks to open and press OK.

Step 3
Select individual site to see detailed site info in the bottom-left pane.

Step 4
Select the 'Sites' tab in the bottom right pane to view all visible sites in the table.
Or export sites to file using 'Export' button in the toolbar.

Find genes regulated by transcription factor

Step 1
Select JunB in 'Transcription factor' parameter to search for genes potentially regulated by JunB.
You also can restrict search to specific cell line and treatment.
Press Run button.

Step 2
Table with genes will open.
SiteCount column specifies the number of ChIP-seq peaks found near this gene.

Step 3
Export genes table to file by pressing 'Export' button in the toolbar.
'Export document' window will appear, press 'OK'.

Step 4
'Export properties' dialog will appear.
Select options that you need and press 'OK'.

v17.04

GTRD Gene Transcription Regulation Database

Workflow How it was constructed?

Statisticsversion 17.04

How to cite

License

Studies citing GTRD

User interface

Overview

Start page

Browse ChIP-seq experiments as table

Browse ChIP-seq experiments in TFClass tree

Integrated genome browser

Find TF binding sites near the specified gene

Find genes potentially regulated by the specified TF

Use cases

Search ChIP-seq experiments by transcription factor

Step 1 Enter TF name into the search box and press enter. Search results will appear in the bottom pane.

Step 2 Click on the experiment to see detailed experiment information in the bottom-left pane.

Step 3 You can use * in the search field for fuzzy matching. Enter stat* to search for any stat TF.

Browse ChIP-seq peaks in genome browser

Step 1 Select 'Organism' and 'ChIP-seq peak calling method'. Press 'Show' button.

Step 2 Genome browser will open. Select additional tracks to open and press OK.

Step 3 Genome browser shows coverage profile for the large number of sites. Zoom in to see individual sites. Press 'Semantic zoom in' button in the toolbar or use Ctrl+Scroll mouse wheel.

Step 4 Zoom in once more to see TF names

Step 5 Select individual site to see detailed site info in the bottom-left pane.

Step 6 Select the 'Sites' tab in the bottom right pane to view all visible sites in the table. Or export sites to file using 'Export' button in the toolbar.

Find transcription factor binding sites on gene

Step 1 To search for c-Jun binding sites near the TP53 gene: enter TP53 into 'Gene symbol' field and select c-Jun transcription factor. You also can restrict search to specific cell line and treatment. Press Run button.

Step 2 Genome browser will open. Select additional tracks to open and press OK.

Step 3 Select individual site to see detailed site info in the bottom-left pane.

Step 4 Select the 'Sites' tab in the bottom right pane to view all visible sites in the table. Or export sites to file using 'Export' button in the toolbar.

Find genes regulated by transcription factor

Step 1 Select JunB in 'Transcription factor' parameter to search for genes potentially regulated by JunB. You also can restrict search to specific cell line and treatment. Press Run button.

Step 2 Table with genes will open. SiteCount column specifies the number of ChIP-seq peaks found near this gene.

Step 3 Export genes table to file by pressing 'Export' button in the toolbar. 'Export document' window will appear, press 'OK'.

Step 4 'Export properties' dialog will appear. Select options that you need and press 'OK'.

GTRD
Gene Transcription Regulation Database

Workflow
How it was constructed?

Statistics
version 17.04

Step 1
Enter TF name into the search box and press enter.
Search results will appear in the bottom pane.

Step 2
Click on the experiment to see detailed experiment information in the bottom-left pane.

Step 3
You can use * in the search field for fuzzy matching.
Enter stat* to search for any stat TF.

Step 1
Select 'Organism' and 'ChIP-seq peak calling method'.
Press 'Show' button.

Step 2
Genome browser will open.
Select additional tracks to open and press OK.

Step 3
Genome browser shows coverage profile for the large number of sites.
Zoom in to see individual sites. Press 'Semantic zoom in' button in the toolbar or use Ctrl+Scroll mouse wheel.

Step 4
Zoom in once more to see TF names

Step 5
Select individual site to see detailed site info in the bottom-left pane.

Step 6
Select the 'Sites' tab in the bottom right pane to view all visible sites in the table.
Or export sites to file using 'Export' button in the toolbar.

Step 1
To search for c-Jun binding sites near the TP53 gene:
enter TP53 into 'Gene symbol' field and select c-Jun transcription factor.
You also can restrict search to specific cell line and treatment.
Press Run button.

Step 2
Genome browser will open.
Select additional tracks to open and press OK.

Step 3
Select individual site to see detailed site info in the bottom-left pane.

Step 4
Select the 'Sites' tab in the bottom right pane to view all visible sites in the table.
Or export sites to file using 'Export' button in the toolbar.

Step 1
Select JunB in 'Transcription factor' parameter to search for genes potentially regulated by JunB.
You also can restrict search to specific cell line and treatment.
Press Run button.

Step 2
Table with genes will open.
SiteCount column specifies the number of ChIP-seq peaks found near this gene.

Step 3
Export genes table to file by pressing 'Export' button in the toolbar.
'Export document' window will appear, press 'OK'.

Step 4
'Export properties' dialog will appear.
Select options that you need and press 'OK'.