Difference between revisions of "GTRD"

Revision as of 18:06, 1 July 2013 (view source) Ivan Yevshin (Talk | contribs) ← Older edit		Revision as of 18:07, 1 July 2013 (view source) Ivan Yevshin (Talk | contribs) Newer edit →
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	Most of ChIP-seq experiments (1638) have corresponding control experiment. [[File:gtrd_exp_control.png|thumb|Control experiments]]		Most of ChIP-seq experiments (1638) have corresponding control experiment. [[File:gtrd_exp_control.png|thumb|Control experiments]]
		+
		+	General statistics:
		+	{| class="wikitable"
		+	|-
		+	! 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.		In average each transcription factor is measured in 4.07 ChIP-seq experiments, but 284 (60%) transcription factors measured only in one experiment.
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	|-		|-
	| GR || 24		| GR || 24
−	|}
−
−	General statistics:
−
−
−	{| class="wikitable"
−	|-
−	! 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
	|}		|}

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Revision as of 18:07, 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