Difference between revisions of "GTRD statistics"

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'''2417''' ChIP-seq experiments for '''470''' distinct sequence specific transcription factors
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== Statistics for version 19.10 (version 19.04) ==
  
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=== Experiments by species ===
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=== ChIP-seq ===
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[[File:GTRD statistics-by-species.png]]
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=== Control experiments ===
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−
[[File:GTRD statistics-control.png]]
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=== Experiments by transcription factor ===
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'''4.07''' experiments per transcription factor in average.
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{| class="wikitable"
−
 
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! Species
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'''284 (60%)''' transcription factors measured only in one experiment.
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! ChIP-seq experiments
−
 
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! Transcription factors
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==== Top 10 transcription factors ====
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! ChIP-seq reads<br />
−
 
+
×10<sup>9</sup>
−
{|
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! Reads aligned<br />
 +
×10<sup>9</sup>
 +
! ChIP-seq peaks<br />
 +
×10<sup>6</sup>
 +
! Clusters<br />
 +
×10<sup>6</sup>
 +
! Metaclusters<br />
 +
×10<sup>6</sup>
 
|-
 
|-
−
!Transcription Factor
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| Arabidopsis thaliana
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!ChIP-seq experiments count
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| 454 <span class="prev_version">(424)</span>
 +
| 124 <span class="prev_version">(120)</span>
 +
| 25.3 <span class="prev_version">(24.2)</span>
 +
| 15.1 <span class="prev_version">(14.4)</span>
 +
| 4.8 <span class="prev_version">(2.9)</span>
 +
| 3.8 <span class="prev_version">(2.2)</span>
 +
| 0.44 <span class="prev_version">(0.38)</span>
 
|-
 
|-
−
|CTCF <nowiki>[</nowiki>11<nowiki>]</nowiki>
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| Caenorhabditis elegans
−
|195
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| 1558 <span class="prev_version">(1508)</span>
 +
| 331 <span class="prev_version">(326)</span>
 +
| 30.5 <span class="prev_version">(26.6)</span>
 +
| 21.5 <span class="prev_version">(19.1)</span>
 +
| 6.2 <span class="prev_version">(3.4)</span>
 +
| 4.5 <span class="prev_version">(2.4)</span>
 +
| 0.5 <span class="prev_version">(0.4)</span>
 
|-
 
|-
−
|c-Myc
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| Danio rerio
−
|45
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| 55 <span class="prev_version">(51)</span>
 +
| 21 <span class="prev_version">(20)</span>
 +
| 2.4 <span class="prev_version">(2.1)</span>
 +
| 1,2 <span class="prev_version">(1.1)</span>
 +
| 2.2 <span class="prev_version">(2.1)</span>
 +
| 2.3 <span class="prev_version">(1.9)</span>
 +
| 0.28 <span class="prev_version">(0.26)</span>
 
|-
 
|-
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|Estrogen receptor α (ERα) (NR3A1)
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| Drosophila melanogaster
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|44
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| 2366 <span class="prev_version">(2182)</span>
 +
| 569 <span class="prev_version">(552)</span>
 +
| 79.8 <span class="prev_version">(74.4)</span>
 +
| 56.8 <span class="prev_version">(53.1)</span>
 +
| 19.3 <span class="prev_version">(10.5)</span>
 +
| 5.4 <span class="prev_version">(7.4)</span>
 +
| 0.7 <span class="prev_version">(1.4)</span>
 
|-
 
|-
−
|REST <nowiki>[</nowiki>1+7+1<nowiki>]</nowiki> (NRSF, XBR)
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| Homo sapiens
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|37
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| 13515 <span class="prev_version">(10675)</span>
 +
| 1339 <span class="prev_version">(1158)</span>
 +
| 783.0 <span class="prev_version">(616.3)</span>
 +
| 606.9 <span class="prev_version">(483.3)</span>
 +
| 1102.3 <span class="prev_version">(818)</span>
 +
| 703.6 <span class="prev_version">(505.2)</span>
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| 91.7 <span class="prev_version">(60.5)</span>
 
|-
 
|-
−
|C/EBPβ (NF-IL6-1)
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| Mus musculus
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|37
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| 10728 <span class="prev_version">(8055)</span>
 +
| 738 <span class="prev_version">(584)</span>
 +
| 577.5 <span class="prev_version">(403.4)</span>
 +
| 381.9 <span class="prev_version">(273.1)</span>
 +
| 943.7 <span class="prev_version">(699.8)</span>
 +
| 598.8 <span class="prev_version">(431.6)</span>
 +
| 80.8 <span class="prev_version">(56.0)</span>
 
|-
 
|-
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|GATA-1 (GF-1, EryF1, NF-E1)
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| Rattus norvegicus
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|33
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| 187 <span class="prev_version">(153)</span>
 +
| 36 <span class="prev_version">(29)</span>
 +
| 9.5 <span class="prev_version">(7.5)</span>
 +
| 6.1 <span class="prev_version">(4.8)</span>
 +
| 11.0 <span class="prev_version">(9.3)</span>
 +
| 9.2 <span class="prev_version">(7.6)</span>
 +
| 1.4 <span class="prev_version">(1.1)</span>
 
|-
 
|-
−
|NF-κB p65 (RelA)
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| Saccharomyces cerevisiae
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|30
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| 1581 <span class="prev_version">(1364)</span>
 +
| 161 <span class="prev_version">(142)</span>
 +
| 25.8 <span class="prev_version">(20.3)</span>
 +
| 19.2 <span class="prev_version">(15.5)</span>
 +
| 1.62 <span class="prev_version">(0.66)</span>
 +
| 0.84 <span class="prev_version">(0.3)</span>
 +
| 0,056 <span class="prev_version">(0.038)</span>
 
|-
 
|-
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|Max
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| Schizosaccharomyces pombe
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|30
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| 226 <span class="prev_version">(222)</span>
 +
| 57 <span class="prev_version">(55)</span>
 +
| 3.5 <span class="prev_version">(3.4)</span>
 +
| 2.6 <span class="prev_version">(2.6)</span>
 +
| 0.249 <span class="prev_version">(0.11)</span>
 +
| 0.18 <span class="prev_version">(0.09)</span>
 +
| 0.014 <span class="prev_version">(0.011)</span>
 
|-
 
|-
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|PU.1 (Spi-1)
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| Total
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|29
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| 30670 <span class="prev_version">(24634)</span>
−
|-
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| 3376 <span class="prev_version">(2986)</span>
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|Glucocorticoid receptor (GR) (NR3C1)
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| 1537.3 <span class="prev_version">(1178.3)</span>
−
|24
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| 1111.3 <span class="prev_version">(867.1)</span>
 +
| 2091.3 <span class="prev_version">(1546.7)</span>
 +
| 1328.6 <span class="prev_version">(958.7)</span>
 +
| 175.9 <span class="prev_version">(120.1)</span>
 
|}
 
|}
  
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=== ChIP-seq peaks ===
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=== DNase-seq ===
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−
{|
+
−
|-
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−
! align="right"|Total:
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−
|5.9515E7
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−
|-
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−
! align="right"|Per experiment in avg.:
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−
|32899
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−
|-
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−
! align="right"|Experiments with peaks:
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−
|1809
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−
|}
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−
[[File:GTRD statistics-peakCounts.png]]
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−
=== Alignment ===
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−
 
+
−
{|
+
−
|-
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−
! align="right"|Total:
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−
|5.8848E10
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−
|-
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! align="right"|Per experiment in avg.:
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−
|2.5675E7
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−
|-
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−
! align="right"|Experiments with alignment:
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−
|2292
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−
|}
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−
[[File:GTRD statistics-alignCounts.png]]
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=== Raw reads ===
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{|
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{| class="wikitable"
 +
!width="25%"| Species
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!width="25%"| DNase-seq experiments
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!width="25%"| DNase I hypersensitive sites (DHSs)<br />
 +
×10<sup>6</sup>
 +
!width="25%"| DNase-seq footprints (FDR<0.01)<br />
 +
×10<sup>6</sup>
 
|-
 
|-
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! align="right"|Total:
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| Homo sapiens
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|8.0808E10
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| 1482 <span class="prev_version">(739)</span>
 +
|
 +
* macs2: 238.2
 +
* hotspot2: 169.2
 +
|
 +
* macs2: 25.90
 +
* hotspot2: 25.07
 
|-
 
|-
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! align="right"|Per experiment in avg.:
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| Mus musculus
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|3.4937E7
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| 103 <span class="prev_version">(103)</span>
 +
|
 +
* macs2: 20.6
 +
* hotspot2: 22.0
 +
|
 +
* macs2: 4.44
 +
* hotspot2: 4.14
 
|-
 
|-
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! align="right"|Experiments with alignment:
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| Total
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|2313
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| 1585 <span class="prev_version">(842)</span>
 +
|
 +
* macs2: 258.8
 +
* hotspot2: 191.2
 +
|
 +
* macs2: 30.34
 +
* hotspot2: 29.21
 
|}
 
|}
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[[File:GTRD statistics-readCounts.png]]
 
−
=== Percent aligned per experiment distribution ===
 
−
[[File:GTRD statistics-percentAligned.png]]
 
−
[[Category:Autogenerated pages]]
 

Latest revision as of 12:10, 8 November 2019

[edit] Statistics for version 19.10 (version 19.04)

[edit] ChIP-seq

Species ChIP-seq experiments Transcription factors ChIP-seq reads

×109

Reads aligned

×109

ChIP-seq peaks

×106

Clusters

×106

Metaclusters

×106

Arabidopsis thaliana 454 (424) 124 (120) 25.3 (24.2) 15.1 (14.4) 4.8 (2.9) 3.8 (2.2) 0.44 (0.38)
Caenorhabditis elegans 1558 (1508) 331 (326) 30.5 (26.6) 21.5 (19.1) 6.2 (3.4) 4.5 (2.4) 0.5 (0.4)
Danio rerio 55 (51) 21 (20) 2.4 (2.1) 1,2 (1.1) 2.2 (2.1) 2.3 (1.9) 0.28 (0.26)
Drosophila melanogaster 2366 (2182) 569 (552) 79.8 (74.4) 56.8 (53.1) 19.3 (10.5) 5.4 (7.4) 0.7 (1.4)
Homo sapiens 13515 (10675) 1339 (1158) 783.0 (616.3) 606.9 (483.3) 1102.3 (818) 703.6 (505.2) 91.7 (60.5)
Mus musculus 10728 (8055) 738 (584) 577.5 (403.4) 381.9 (273.1) 943.7 (699.8) 598.8 (431.6) 80.8 (56.0)
Rattus norvegicus 187 (153) 36 (29) 9.5 (7.5) 6.1 (4.8) 11.0 (9.3) 9.2 (7.6) 1.4 (1.1)
Saccharomyces cerevisiae 1581 (1364) 161 (142) 25.8 (20.3) 19.2 (15.5) 1.62 (0.66) 0.84 (0.3) 0,056 (0.038)
Schizosaccharomyces pombe 226 (222) 57 (55) 3.5 (3.4) 2.6 (2.6) 0.249 (0.11) 0.18 (0.09) 0.014 (0.011)
Total 30670 (24634) 3376 (2986) 1537.3 (1178.3) 1111.3 (867.1) 2091.3 (1546.7) 1328.6 (958.7) 175.9 (120.1)

[edit] DNase-seq

Species DNase-seq experiments DNase I hypersensitive sites (DHSs)

×106

DNase-seq footprints (FDR<0.01)

×106

Homo sapiens 1482 (739)
  • macs2: 238.2
  • hotspot2: 169.2
  • macs2: 25.90
  • hotspot2: 25.07
Mus musculus 103 (103)
  • macs2: 20.6
  • hotspot2: 22.0
  • macs2: 4.44
  • hotspot2: 4.14
Total 1585 (842)
  • macs2: 258.8
  • hotspot2: 191.2
  • macs2: 30.34
  • hotspot2: 29.21
Retrieved from "https://wiki.biouml.org/index.php?title=GTRD_statistics&oldid=8432"
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