Difference between revisions of "GTRD comparison"

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! 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 ( * - and others ) !! Number of TF ( * - and others ) !! 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 v18.06 || total: 17485 <br/> human: 7239 || total: 2399 <br/> human: 852 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana || MACS, 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: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No
 
|-
 
|-
 
| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || H. sapiens, M. musculus || MACS2 || No
 
| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || H. sapiens, M. musculus || MACS2 || No
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| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)
 
| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)
 
|-
 
|-
| 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: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans || SPP, GEM, PeakSeq, MACS || No
 
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|-
| 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: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus || >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
 
| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || H. sapiens, M. musculus || None || No
 
|-
 
|-
| 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
+
| NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes || None || No
 
|}
 
|}
  
 
<nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.
 
<nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.

Revision as of 11:20, 13 November 2018

Database Number of TF ChIP-seq samples ( * - and others ) Number of TF ( * - and others ) Species ChIP-seq peak callers Metacluster approach
GTRD v18.06 total: 17485
human: 7239
total: 2399
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
ChIP-Atlas total: 19414*
human: 8368*
total: 1929
human: 820
H. sapiens, M. musculus, R. norvegicus,
D. melanogaster, C. elegans, S. cerevisiae
MACS2 No
Cistrome DB total: 20408*
human: 11348*
total: Unknown
human: Unknown
H. sapiens, M. musculus MACS2 No
ReMap 2018 total: 2829*
human: 2829*
total: 485
human: 485
H. sapiens MACS2 Yes (CRMs)
ENCODE total: 3684
human: 2489
total: Unknown
human: Unknown
H. sapiens, M. musculus, D. melanogaster,
C. elegans
SPP, GEM, PeakSeq, MACS No
ChIPBase total: 4290
human: 2498
total: Unknown
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
Factorbook total: 1007
human: 837
total: 167
human: 51
H. sapiens, M. musculus None 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

*The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.

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