GTRD statistics - Revision history

WikiBot at 05:10, 8 November 2019

2019-11-08T05:10:07Z

2019-11-08T05:08:38Z

2019-11-08T05:02:57Z

2017-11-29T10:45:04Z

2017-10-27T05:40:42Z

2017-02-13T11:58:46Z

Automatic synchronization with BioUML

2016-08-26T10:47:06Z

2016-08-26T10:46:05Z

‎Experiments by species

2016-08-26T10:45:53Z

‎Control experiments

2016-08-26T10:45:40Z

‎Control experiments

@@ Line 109: / Line 109: @@
 |}
-=== DNase-seq (version 18.06) ===
+=== DNase-seq ===
 {| class="wikitable"

@@ Line 3: / Line 3: @@
 === ChIP-seq ===
-{|
+{| class="wikitable"
 ! Species
 ! ChIP-seq experiments
@@ Line 111: / Line 111: @@
 === DNase-seq (version 18.06) ===
-{|
+{| class="wikitable"
 !width="25%"| Species
 !width="25%"| DNase-seq experiments

@@ 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.
-=== Experiments by species ===
+====Summary of ChIP-seq experiments====
-[[File:GTRD statistics-by-species2.png|600px]]
+{| class="wikitable"
-=== Control experiments ===
+====Summary of transcription factors====
-[[File:GTRD statistics-control2.png|600px]]
+{| class="wikitable"
 ==== Top 10 transcription factors ====
@@ Line 19: / Line 35: @@
 ! 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
 |-
-| 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
 |}

@@ Line 1: / Line 1: @@
-== Error ==
+'''5072''' ChIP-seq experiments for '''476''' human and '''257''' mouse TFs that correspond to '''542''' TFClass classes.
-Cannot retrieve element: databases/GTRD/Data/statistics/index.html
+=== Experiments by species ===
-Reason: Element not found: databases/GTRD/Data/statistics
+=== Control experiments ===
-[[Category:Autogenerated pages]]
+[[File:GTRD statistics-control2.png|600px]]

@@ Line 1: / Line 1: @@
-'''5072''' ChIP-seq experiments for '''476''' human and '''257''' mouse TFs that correspond to '''542''' TFClass classes.
+== Error ==
-=== Experiments by species ===
+Cannot retrieve element: databases/GTRD/Data/statistics/index.html
-[[File:GTRD statistics-by-species2.png|600px]]
-−
-=== Control experiments ===
-[[File:GTRD statistics-control2.png|600px]]
-−
-=== Experiments by transcription factor ===
-−
-'''9.37''' experiments per transcription factor in average.
-−
-% of TFs have been measured in more than one experiment.
-−
-==== Top 10 transcription factors ====
-−
-{| class="wikitable"
-|-
-! Transcription Factor !! Number of ChIP-seq experiments
-|-
-| CTCF || 282
-|-
-| AR || 117
-|-
-| PU.1 || 103
-|-
-| ERα || 92
-|-
-| c-Myc || 79
-|-
-| C/EBPβ || 74
-|-
-| NF-κB p65 || 70
-|-
-| GR || 53
-|-
-| REST || 51
-|-
-| GATA-1 || 51
-|}
 [[Category:Autogenerated pages]]

← Older revision		Revision as of 10:47, 26 August 2016
Line 40:		Line 40:
	\|}		\|}

−
−	~~=== ChIP-seq peaks ===~~
−
−	{\|
−	\|-
−	~~! align="right"\|Total:~~
−	~~\|5.9515E7~~
−	\|-
−	~~! align="right"\|Per experiment in avg.:~~
−	~~\|32899~~
−	\|-
−	~~! align="right"\|Experiments with peaks:~~
−	~~\|1809~~
−	\|}
−	~~[[File:GTRD statistics-peakCounts.png]]~~
−	~~=== Alignment ===~~
−
−	{\|
−	\|-
−	~~! align="right"\|Total:~~
−	~~\|5.8848E10~~
−	\|-
−	~~! align="right"\|Per experiment in avg.:~~
−	~~\|2.5675E7~~
−	\|-
−	~~! align="right"\|Experiments with alignment:~~
−	~~\|2292~~
−	\|}
−	~~[[File:GTRD statistics-alignCounts.png]]~~
−	~~=== Raw reads ===~~
−
−	{\|
−	\|-
−	~~! align="right"\|Total:~~
−	~~\|8.0808E10~~
−	\|-
−	~~! align="right"\|Per experiment in avg.:~~
−	~~\|3.4937E7~~
−	\|-
−	~~! align="right"\|Experiments with alignment:~~
−	~~\|2313~~
−	\|}
−	~~[[File:GTRD statistics-readCounts.png]]~~
−	~~=== Percent aligned per experiment distribution ===~~
−	~~[[File:GTRD statistics-percentAligned.png]]~~
	[[Category:Autogenerated pages]]		[[Category:Autogenerated pages]]

@@ Line 5: / Line 5: @@
 === Control experiments ===
-[[File:GTRD statistics-control2.png]]
+[[File:GTRD statistics-control2.png|400px]]
 === Experiments by transcription factor ===