Difference between revisions of "GTRD"

From BioUML platform
Jump to: navigation, search
Line 40: Line 40:
 
*'''ChIP-seq reads''' total 80.808E9, per experiment in average 34.937E6.
 
*'''ChIP-seq reads''' total 80.808E9, per experiment in average 34.937E6.
 
*'''Read alignments''' total 58.848E9, per experiment in average: 25.675E6.
 
*'''Read alignments''' total 58.848E9, per experiment in average: 25.675E6.
 +
*'''ChIP-seq peaks''' total 59.515E6, per experiment in average: 32899.

Revision as of 18:00, 1 July 2013

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

The web interface to GTRD is freely 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

In average each transcription factor is measured in 4.07 ChIP-seq experiments, but 284 (60%) transcription factors measured only in only 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
  • ChIP-seq reads total 80.808E9, per experiment in average 34.937E6.
  • Read alignments total 58.848E9, per experiment in average: 25.675E6.
  • ChIP-seq peaks total 59.515E6, per experiment in average: 32899.
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox