Difference between revisions of "GTRD"

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		+	==Database structure==
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		+	==Web interface to database==

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Revision as of 18:22, 1 July 2013

GTRD (Gene Transcription Regulation Database) is a database of transcription factor binding sites identified from ChIP-seq experiments. GTRD analyze freely avalable ChIP-seq experiments from literature, GEO, SRA and ENCODE databases.

The web interface to GTRD is available at http://192.168.199.241/bioumlweb/#anonymous=true&perspective=GTRD.

Database statistics

GTRD uses 2417 ChIP-seq experiments for 470 distinct sequence specific transcription factors. Most of ChIP-seq experiments (1638) have corresponding control experiment.

General statistics:

Object type	Total count	Per ChIP-seq experiment
ChIP-seq reads	80.808E9	34.937E6
Read alignments	58.848E9	25.675E6
ChIP-seq peaks	59.515E6	32899

In average each transcription factor is measured in 4.07 ChIP-seq experiments, but 284 (60%) transcription factors measured only in one experiment.

The ten most studied transcription factors listed bellow:

Transcription Factor	Number of ChIP-seq experiments
CTCF	195
c-Myc	45
ERα	44
NRSF	37
C/EBPβ	37
GATA-1	33
NF-κB p65	30
Max	30
PU.1	29
GR	24

Database structure

Web interface to database