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.
