Difference between revisions of "GTRD statistics"

From BioUML platform
Jump to: navigation, search
Line 1: Line 1:
−
'''5072''' ChIP-seq experiments for '''476''' human and '''257''' mouse TFs that correspond to '''542''' TFClass classes.
+
Currently GTRD (v17.11) indexes 12168 ChIP-seq experiments on sequence specific transcription factors for human, mouse and rat.
 +
Some of the experiments indexed in GTRD were not processed by our unified workflow for different reasons, so such experiments only present in the GTRD metadata part but not in the peaks and clusters part.  
  
−
=== Experiments by species ===
+
====Summary of ChIP-seq experiments====
−
[[File:GTRD statistics-by-species2.png|600px]]
+
{| class="wikitable"
 +
|-
 +
! Species !! Indexed ChIP-seq experiments !! Indexed control ChIP-seq experiments !! Processed ChIP-seq experiments || Processed control ChIP-seq experiments
 +
|-
 +
| Human || 5143 || 1676 || 4236 || 1367
 +
|-
 +
| Mouse || 3751 || 1501 || 3488 || 1327
 +
|-
 +
| Rat || 74 || 23 || 0 || 0
 +
|-
 +
| Total || 8968 || 3200 || 7724 || 2694
 +
|}
  
−
=== Control experiments ===
+
====Summary of transcription factors====
−
[[File:GTRD statistics-control2.png|600px]]
+
{| class="wikitable"
 +
|-
 +
! Species !! Indexed transcription factors !! Processed transcription factors
 +
|-
 +
| Human || 819 || 682
 +
|-
 +
| Mouse || 402 || 384
 +
|-
 +
| Distinct TFClasses for Human+Mouse || 900 || 766
 +
|}
  
−
=== Experiments by transcription factor ===
 
−
 
−
'''9.37''' experiments per transcription factor in average.
 
−
 
−
54% of TFs have been measured in more than one experiment.
 
  
 
==== Top 10 transcription factors ====
 
==== Top 10 transcription factors ====
Line 19: Line 35:
 
! Transcription Factor !! Number of ChIP-seq experiments
 
! Transcription Factor !! Number of ChIP-seq experiments
 
|-
 
|-
−
| CTCF || 282
+
| CTCF || 635
 
|-
 
|-
−
| AR || 117
+
| ERα || 286
 
|-
 
|-
−
| PU.1 || 103
+
| AR || 275
 
|-
 
|-
−
| ERα || 92
+
| c-Myc || 204
 +
|-
 +
| PU.1 || 194
 +
|-
 +
| p65 || 158
 +
|-
 +
| C/EBPβ || 152
 +
|-
 +
| GR || 147
 +
|-
 +
| FOXA1 || 141
 +
|-
 +
| p53 || 119
 +
|}
 +
 
 +
==== Data summary ====
 +
 
 +
{| class="wikitable"
 
|-
 
|-
−
| c-Myc || 79
+
! Data type !! Count
 
|-
 
|-
−
| C/EBPβ || 74
+
| ChIP-seq reads || 508 023 543 763
 
|-
 
|-
−
| NF-κB p65 || 70
+
| Reads aligned || 335 707 127 761
 
|-
 
|-
−
| GR || 53
+
| ChIP-seq peaks || 961 923 622
 
|-
 
|-
−
| REST || 51
+
| Clusters || 527 498 674
 
|-
 
|-
−
| GATA-1 || 51
+
| Metaclusters || 70 338 813
 
|}
 
|}

Revision as of 17:45, 29 November 2017

Currently GTRD (v17.11) indexes 12168 ChIP-seq experiments on sequence specific transcription factors for human, mouse and rat. Some of the experiments indexed in GTRD were not processed by our unified workflow for different reasons, so such experiments only present in the GTRD metadata part but not in the peaks and clusters part.

Contents

Summary of ChIP-seq experiments

Species Indexed ChIP-seq experiments Indexed control ChIP-seq experiments Processed ChIP-seq experiments Processed control ChIP-seq experiments
Human 5143 1676 4236 1367
Mouse 3751 1501 3488 1327
Rat 74 23 0 0
Total 8968 3200 7724 2694

Summary of transcription factors

Species Indexed transcription factors Processed transcription factors
Human 819 682
Mouse 402 384
Distinct TFClasses for Human+Mouse 900 766


Top 10 transcription factors

Transcription Factor Number of ChIP-seq experiments
CTCF 635
ERα 286
AR 275
c-Myc 204
PU.1 194
p65 158
C/EBPβ 152
GR 147
FOXA1 141
p53 119

Data summary

Data type Count
ChIP-seq reads 508 023 543 763
Reads aligned 335 707 127 761
ChIP-seq peaks 961 923 622
Clusters 527 498 674
Metaclusters 70 338 813
Retrieved from "https://wiki.biouml.org/index.php?title=GTRD_statistics&oldid=7546"
Personal tools
Namespaces

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