Difference between revisions of "GTRD comparison"

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{| class="wikitable"
 
{| class="wikitable"
! Database !! Number of TF ChIP-seq samples ( * - and others ) !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach
+
! Database !! Number of TF ChIP-seq samples <br/>!! Number of TFs !! Species !! ChIP-seq peak callers !! Metacluster approach
 
|-
 
|-
| GTRD v18.06 || total: 17485 <br/> human: 7239 || total: 2399 <br/> human: 852 || H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, D. rerio, S. pombe, S. cerevisiae, A. thaliana || MACS, SISSRs, GEM, PICS || Yes   
+
| GTRD v19.10 || total: 30670* <br/> human: 13515* || total: 3376* <br/> human: 1339* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, SISSRs, GEM, PICS || Yes   
 
|-
 
|-
| ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No
+
| ChIP-Atlas || total: 22872* <br/> human: 10129* || total: 1972* <br/> human: 878* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No
 
|-
 
|-
| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || H. sapiens, M. musculus || MACS2 || No
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| Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No
 
|-
 
|-
| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)
+
| NGS-QC || total: 22398* <br/> human: 11597* || total: Unkonwn <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</i> || None || No
 
|-
 
|-
| ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, C. elegans || SPP, GEM, PeakSeq, MACS || No
+
| ENCODE || total: 3609* <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No
 
|-
 
|-
| ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, D. rerio, X. tropicalis, C. elegans, D. melanogaster, S. cerevisiae, A. thaliana, G. gallus || >10 in total, but no uniform pipeline, each ChIP-seq is processed by different peak caller  || No
+
| ChIPBase || total: 4300 <br/> human: 2498 || total: 870 <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No
 
|-
 
|-
| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || H. sapiens, M. musculus || None || No
+
| ReMap 2018 v1.2 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <i>H. sapiens</i> || MACS2 || Yes (CRMs)
 
|-
 
|-
| NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, D. rerio, C. elegans, D. melanogaster, S. cerevisiae, A. thaliana, G. gallus, P. troglodytes || None || No
+
| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No
 
|}
 
|}
 
+
<nowiki>*</nowiki> TFs and others (without histone modifications).
<nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.
+
<br/><nowiki>**</nowiki> The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.

Latest revision as of 12:45, 8 November 2019

Database Number of TF ChIP-seq samples
Number of TFs Species ChIP-seq peak callers Metacluster approach
GTRD v19.10 total: 30670*
human: 13515*
total: 3376*
human: 1339*
H. sapiens, M. musculus, R. norvegicus,
D. melanogaster, C. elegans, D. rerio,
S. pombe, S. cerevisiae, A. thaliana
MACS2, SISSRs, GEM, PICS Yes
ChIP-Atlas total: 22872*
human: 10129*
total: 1972*
human: 878*
H. sapiens, M. musculus, R. norvegicus,
D. melanogaster, C. elegans, S. cerevisiae
MACS2 No
Cistrome DB total: 24065*
human: 13976*
total: Unknown
human: Unknown
H. sapiens, M. musculus MACS2 No
NGS-QC total: 22398*
human: 11597*
total: Unkonwn
human: Unknown
H. sapiens, M. musculus, R. norvegicus,
D. rerio, C. elegans, D. melanogaster,
S. cerevisiae, A. thaliana, G. gallus,
P. troglodytes
None No
ENCODE total: 3609*
human: 2407
total: Unknown
human: Unknown
H. sapiens, M. musculus, D. melanogaster,
C. elegans
SPP No
ChIPBase total: 4300
human: 2498
total: 870
human: Unknown
H. sapiens, M. musculus, R. norvegicus,
D. rerio, X. tropicalis, C. elegans,
D. melanogaster, S. cerevisiae, A. thaliana,
G. gallus
>10 in total, but no uniform pipeline,
each ChIP-seq is processed by different peak caller
No
ReMap 2018 v1.2 total: 2829*
human: 2829*
total: 485
human: 485
H. sapiens MACS2 Yes (CRMs)
Factorbook total: 1007
human: 837
total: 167
human: 51
H. sapiens, M. musculus None No

* TFs and others (without histone modifications).
** The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.

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