Difference between revisions of "GTRD comparison"

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<nowiki>*</nowiki>TFs and others (without histone modifications).
 
<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.

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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