Difference between revisions of "GTRD comparison"
From BioUML platform
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| − | ! Database !! Number of TF ChIP-seq samples | + | ! Database !! Number of TF ChIP-seq samples !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach |
|- | |- | ||
| GTRD v19.10 || total: 30670 <br/> human: 13515 || total: 3376 <br/> human: 1339 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana || MACS2, SISSRs, GEM, PICS || Yes | | GTRD v19.10 || total: 30670 <br/> human: 13515 || total: 3376 <br/> human: 1339 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana || MACS2, SISSRs, GEM, PICS || Yes | ||
Revision as of 10:58, 8 November 2019
| Database | Number of TF ChIP-seq samples | Number of TF ( * - and others ) | 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: 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 | 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.
