Difference between revisions of "GTRD statistics"

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Currently GTRD (v17.11) indexes 12168 ChIP-seq experiments on sequence specific transcription factors for human, mouse and rat.
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== Statistics for version 19.10 (version 19.04) ==
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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.
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====Summary of ChIP-seq experiments====
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=== ChIP-seq ===
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{| class="wikitable"
+
−
|-
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−
! Species !! Indexed ChIP-seq experiments !! Indexed control ChIP-seq experiments !! Processed ChIP-seq experiments || Processed control ChIP-seq experiments
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−
|-
+
−
| Human || 5143 || 1676 || 4236 || 1367
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−
|-
+
−
| Mouse || 3751 || 1501 || 3488 || 1327
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−
|-
+
−
| Rat || 74 || 23 || 0 || 0
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−
|-
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−
| Total || 8968 || 3200 || 7724 || 2694
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−
|}
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====Summary of transcription factors====
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{|
−
{| class="wikitable"
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! Species
 +
! ChIP-seq experiments
 +
! Transcription factors
 +
! ChIP-seq reads<br />
 +
×10<sup>9</sup>
 +
! 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>
 
|-
 
|-
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! Species !! Indexed transcription factors !! Processed transcription factors
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| Arabidopsis thaliana
 +
| 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>
 
|-
 
|-
−
| Human || 819 || 682
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| Caenorhabditis elegans
 +
| 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>
 
|-
 
|-
−
| Mouse || 402 || 384
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| Danio rerio
 +
| 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>
 
|-
 
|-
−
| Distinct TFClasses for Human+Mouse || 900 || 766
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| Drosophila melanogaster
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|}
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| 2366 <span class="prev_version">(2182)</span>
−
 
+
| 569 <span class="prev_version">(552)</span>
−
 
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| 79.8 <span class="prev_version">(74.4)</span>
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==== Top 10 transcription factors ====
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| 56.8 <span class="prev_version">(53.1)</span>
−
 
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| 19.3 <span class="prev_version">(10.5)</span>
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{| class="wikitable"
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| 5.4 <span class="prev_version">(7.4)</span>
 +
| 0.7 <span class="prev_version">(1.4)</span>
 
|-
 
|-
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! Transcription Factor !! Number of ChIP-seq experiments
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| Homo sapiens
 +
| 13515 <span class="prev_version">(10675)</span>
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| 1339 <span class="prev_version">(1158)</span>
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| 783.0 <span class="prev_version">(616.3)</span>
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| 606.9 <span class="prev_version">(483.3)</span>
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| 1102.3 <span class="prev_version">(818)</span>
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| 703.6 <span class="prev_version">(505.2)</span>
 +
| 91.7 <span class="prev_version">(60.5)</span>
 
|-
 
|-
−
| CTCF || 635
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| Mus musculus
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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>
 
|-
 
|-
−
| ERα || 286
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| Rattus norvegicus
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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>
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| 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>
 
|-
 
|-
−
| AR || 275
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| Saccharomyces cerevisiae
 +
| 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>
 
|-
 
|-
−
| c-Myc || 204
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| Schizosaccharomyces pombe
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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>
 
|-
 
|-
−
| PU.1 || 194
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| Total
−
|-
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| 30670 <span class="prev_version">(24634)</span>
−
| p65 || 158
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| 3376 <span class="prev_version">(2986)</span>
−
|-
+
| 1537.3 <span class="prev_version">(1178.3)</span>
−
| C/EBPβ || 152
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| 1111.3 <span class="prev_version">(867.1)</span>
−
|-
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| 2091.3 <span class="prev_version">(1546.7)</span>
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| GR || 147
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| 1328.6 <span class="prev_version">(958.7)</span>
−
|-
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| 175.9 <span class="prev_version">(120.1)</span>
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| FOXA1 || 141
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−
|-
+
−
| p53 || 119
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|}
 
|}
  
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==== Data summary ====
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=== DNase-seq (version 18.06) ===
  
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{| class="wikitable"
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{|
−
|-
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!width="25%"| Species
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! Data type !! Count
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!width="25%"| DNase-seq experiments
−
|-
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!width="25%"| DNase I hypersensitive sites (DHSs)<br />
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| ChIP-seq reads || 508 023 543 763
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×10<sup>6</sup>
−
|-
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!width="25%"| DNase-seq footprints (FDR<0.01)<br />
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| Reads aligned || 335 707 127 761
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×10<sup>6</sup>
 
|-
 
|-
−
| ChIP-seq peaks || 961 923 622
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| Homo sapiens
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| 1482 <span class="prev_version">(739)</span>
 +
|
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* macs2: 238.2
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* hotspot2: 169.2
 +
|
 +
* macs2: 25.90
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* hotspot2: 25.07
 
|-
 
|-
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| Clusters || 527 498 674
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| Mus musculus
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| 103 <span class="prev_version">(103)</span>
 +
|
 +
* macs2: 20.6
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* hotspot2: 22.0
 +
|
 +
* macs2: 4.44
 +
* hotspot2: 4.14
 
|-
 
|-
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| Metaclusters || 70 338 813
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| Total
 +
| 1585 <span class="prev_version">(842)</span>
 +
|
 +
* macs2: 258.8
 +
* hotspot2: 191.2
 +
|
 +
* macs2: 30.34
 +
* hotspot2: 29.21
 
|}
 
|}

Revision as of 12:02, 8 November 2019

Statistics for version 19.10 (version 19.04)

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)

DNase-seq (version 18.06)

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=8429"
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