Difference between revisions of "GTRD comparison"
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{| class="wikitable" | {| class="wikitable" | ||
| − | ! Database !! Number of TF | + | ! Database !! Number of TF ChIP-seq samples <br/>!! Number of TFs !! Species !! ChIP-seq peak callers !! Metacluster approach |
|- | |- | ||
| − | | GTRD v19.10 || total: | + | | GTRD v19.10 || total: 30670* <br/> human: 13515* || total: 3376* <br/> human: 1339* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, SISSRs, GEM, PICS || Yes |
|- | |- | ||
| ChIP-Atlas || total: 22872* <br/> human: 10129* || total: 1972* <br/> human: 878* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No | | ChIP-Atlas || total: 22872* <br/> human: 10129* || total: 1972* <br/> human: 878* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No | ||
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| Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No | | Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No | ||
|- | |- | ||
| − | | | + | | NGS-QC || total: 22398* <br/> human: 11597* || total: Unkonwn <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</i> || None || No |
|- | |- | ||
| − | | ENCODE || total: 3609 <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No | + | | ENCODE || total: 3609* <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No |
|- | |- | ||
| ChIPBase || total: 4300 <br/> human: 2498 || total: 870 <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller || No | | ChIPBase || total: 4300 <br/> human: 2498 || total: 870 <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller || No | ||
|- | |- | ||
| − | | | + | | ReMap 2018 v1.2 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <i>H. sapiens</i> || MACS2 || Yes (CRMs) |
|- | |- | ||
| − | | | + | | Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No |
|} | |} | ||
| − | + | <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. |
Latest 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.
