Difference between revisions of "GTRD"

Revision as of 19:03, 1 July 2013 (view source) Ivan Yevshin (Talk | contribs) ← Older edit		Revision as of 19:09, 1 July 2013 (view source) Ivan Yevshin (Talk | contribs) Newer edit →
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	| ChIP-seq reads || 80.808E9 || 34.937E6		| ChIP-seq reads || 80.808E9 || 34.937E6
	|-		|-
−	| ReadS aligned || 58.848E9 || 25.675E6	+	| Reads aligned || 58.848E9 || 25.675E6
	|-		|-
	| ChIP-seq peaks || 59.515E6 || 32899		| ChIP-seq peaks || 59.515E6 || 32899
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	The 'hub' table provides relations between different GTRD entries.		The 'hub' table provides relations between different GTRD entries.
		+	GTRD uses following identifiers:
		+	{| class="wikitable"
		+	|-
		+	! Template !! Object type || Example
		+	|-
		+	| EXPXXXXXX || ChIP-seq experiment || EXP000489
		+	|-
		+	| READSXXXXXX || Collection of ChIP-seq reads || READS000770
		+	|-
		+	| ALIGNSXXXXXX || Collection of read alignments || ALIGNS010001
		+	|-
		+	| PEAKSXXXXXX || Collection of ChIP-seq peaks || PEAKS010000
		+	|}
		+
	==Web interface to database==		==Web interface to database==

---

Revision as of 19:09, 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
Reads aligned	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

The metadata concerning GTRD is stored in MySQL tables.

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

Column	Description	Example value
id	Unique experiment identifier	EXP000489
antibody	Antibody used in chromatin immunoprecipitation	sc-345
tfClassId	Id in TFClass[1] database of target transcription factor, NULL for control experiments	6.2.1.0.1
cell_line	Studied cell line	HeLa S3
specie	Specie latin name	Homo sapiens
treatment	Cell treatment or conditions	IFN gamma
control_id	Id of control experiment, NULL for control experiments or experiments without control	EXP000490

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

Column	Description	Example values
id	Experiment identifier	EXP000489
external_db	External database name	GEO or PUBMED or ENCODE or SRA
external_db_id	Identifier in external database	GSM320736

The 'hub' table provides relations between different GTRD entries. GTRD uses following identifiers:

Template	Object type	Example
EXPXXXXXX	ChIP-seq experiment	EXP000489
READSXXXXXX	Collection of ChIP-seq reads	READS000770
ALIGNSXXXXXX	Collection of read alignments	ALIGNS010001
PEAKSXXXXXX	Collection of ChIP-seq peaks	PEAKS010000

Web interface to database