Difference between revisions of "GTRD comparison"
From BioUML platform
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! Database !! Number of TF ChIP-seq samples !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach | ! 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 || <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: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No | + | | ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No |
|- | |- | ||
| − | | Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus || MACS2 || No | + | | Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No |
|- | |- | ||
| − | | ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs) | + | | ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <i>H. sapiens</i> || MACS2 || Yes (CRMs) |
|- | |- | ||
| − | | ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans || SPP || No | + | | ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No |
|- | |- | ||
| − | | ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller || No | + | | ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <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 |
|- | |- | ||
| − | | Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || H. sapiens, M. musculus || None || No | + | | Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No |
|- | |- | ||
| − | | NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes || None || 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 |
|} | |} | ||
<nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct. | <nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct. | ||
Revision as of 11:00, 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.
