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
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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