Table 1.
Comparison of the GTRD with other databases on ChIP-seq experiments
| Database | Number of TF ChIP-seq experiments | Number of TFs | ChIP-seq peak callers | Species |
|---|---|---|---|---|
| GTRD v20.06 | total: 35 719 H. sapiens: 15 982 | total: 3 599 H. sapiens: 1391 | MACS2, MACS, GEM, PICS, SISSRs | H. sapiens, M. musculus, R. norvegicus,D. melanogaster, C. elegans, D. rerio, S. pombe, S. cerevisiae, A. thaliana |
| ChIP-Atlas | total: 30 495*H. sapiens: 13 558* | total: 1 781**H. sapiens: 1 020** | MACS2 | H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae |
| CistromeDB | total: 24 065**H. sapiens: 13 976** | total: 1654**H. sapiens: 1470** | MACS2 | H. sapiens, M. musculus |
| ENCODE | total: 3 816 H. sapiens: 2 632 | total: 2 160 H. sapiens: 964 | SPP | H. sapiens, M. musculus, D. melanogaster, C. elegans |
| ChIPBase | total: 4300**H. sapiens: 2498** | total: 870**H. sapiens: 480** | no uniform pipeline, each ChIP-seq is processed by different peak caller | H. sapiens, M. musculus, R. norvegicus,D. rerio, X. tropicalis, C. elegans,D. melanogaster, S. cerevisiae, A. thaliana, G. gallus |
| ReMap 2020 3rd release | total: 6307**H. sapiens: 5798** | total: 1507**H. sapiens: 1135** | MACS2 | H. sapiens, A. thaliana |
| Factorbook | total: 1886**H. sapiens: 1813** | total: 682**H. sapiens: 682** | None | H. sapiens, M. musculus |
*‘TF and others’ according to ChIP-Atlas info. 7 374 input files for human and 17 914 input files in total given in a separate category in ChIP-Atlas are not taken into account in the table as they are not assigned to particular ChIP-Seq data.
**TFs and other DNA binding proteins excluding polymerases and histones.