Difference between revisions of "GTRD comparison"
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Ivan Yevshin (Talk | contribs) |
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!Genome browser | !Genome browser | ||
|- | |- | ||
| − | |GTRD | + | |GTRD v18.01 ([[http://gtrd.biouml.org]]) |
|GEO, SRA, ENCODE | |GEO, SRA, ENCODE | ||
|total 10418, human 5603, mouse 4815 | |total 10418, human 5603, mouse 4815 | ||
Revision as of 16:00, 6 February 2018
| Database, URL | Source of human and mouse data | Number of samples (TF-related)* | Number of TFs | Number of ChIP-seq peak callers used | Metacluster approach | Uniform data processing | Genome browser |
|---|---|---|---|---|---|---|---|
| GTRD v18.01 ([[1]]) | GEO, SRA, ENCODE | total 10418, human 5603, mouse 4815 | 682 human and 384 mouse sequence specific TFs, corresponding to 766 TFClass classes. | 4 (MACS, SISSRs, GEM, PICS) | Yes | Yes | Self-developed |
| ReMap 2018 ([[2]]) | GEO, ENCODE, ARRAYEXPRESS | 3549 human | 486 TFs and non-TFs | MACS2 | Yes(CRMs) | Yes | UCSC, ENSEMBL, Track Hub, IGV |
| ChIPBase ([[3]]) | GEO, ENCODE | total 3549 human 2498 mouse 1036 rat 15 | 252 TFs and non-TFs for 10 species | >10 in total, but no uniform pipeline, each ChIP-seq is processed by different peak caller | No | No | Self-developed: deepView genomeView |
| Cistrome DB ([[4]]) | GEO, SRA, ENA, ENCODE | total 10 276 (TF+non-TF) human 5774 mouse 4502 rat 0 | 260 TFs and non-TFs | 1 (MACS2) | No | Yes | UCSC genome browser |
| ENCODE ([[5]]) | ENCODE | total 1448 human 1254 mouse 194 rat 0 | 295 TFs and non-TFs for human, 52 TFs and non-TFs for mouse | 5 (SPP, GEM, PeakSeq, MACS, Hotspot/Hotspot2) | No | Yes | Self-developed: UCSC genome browser and WashU epigenome browser |
| Factorbook ([[6]]) | ENCODE | total 1007 human 837 mouse 170 rat 0 | 167 TFs, co-factors and chromatin remodeling factors for human, 51—for mouse | None | No | No | No |
| ChIP-Atlas ([[7]]) | SRA | total 10 774 human 5914 mouse 4860 rat 0 | 699 human and 502 mouse TFs and others. | 1(MACS2) | No | Yes | IGV |
| GeneProf ([[8]]) | SRA, ENCODE, literature | total 1692 human 693 mouse 999 rat 0 | 133 human and 131 mouse TFs | 1(MACS) | No | Yes | Self-developed: based on GenomeGraphs |
| NGS-QC ([[9]]) | GEO | total 6672 human 4234 mouse 2438 rat 0 | unknown | None | No | Yes | No |
*The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.
