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.
