Difference between revisions of "GTRD comparison"

! Database !! Number of TF ChIP-seq samples ( * - and others ) !! 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   

| 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

| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || H. sapiens, M. musculus || MACS2 || No

| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || 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

| 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

| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || H. sapiens, M. musculus || 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

 

<nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.