Difference between revisions of "GTRD"

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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
 +
|-
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| ALIGNSXXXXXX || Collection of read alignments || ALIGNS010001
 +
|-
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| PEAKSXXXXXX || Collection of ChIP-seq peaks || PEAKS010000
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|}
 +
  
 
==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.
ChIP-seq experiments by species
Most of ChIP-seq experiments (1638) have corresponding control experiment.
Control experiments

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

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