GTRD

v18.01

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 was it 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 18.01

3340 new 12168 ChIP-seq experiments
53 new 766 Transcription factors
27% new 508 023 543 763 ChIP-seq reads
29% new 335 707 127 761 Reads aligned
31% new 961 923 622 ChIP-seq peaks
20% new 527 498 674 Clusters
14% new 70 338 813 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.

v18.01

GTRD
Gene Transcription Regulation Database

Workflow
How was it constructed?

Statistics
version 18.01

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'.

v18.01

GTRD Gene Transcription Regulation Database

Workflow How was it constructed?

Statisticsversion 18.01

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 was it constructed?

Statistics
version 18.01

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'.