Difference between revisions of "GTRD comparison"

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|Yes  
 
|Yes  
 
|Self-developed  
 
|Self-developed  
 +
|-
 +
|ReMap 2018 ([[http://remap.cisreg.eu]])
 +
|GEO, ENCODE, ARRAYEXPRESS
 +
|3549 human
 +
|486 TFs and non-TFs
 +
|MACS2
 +
|Yes(CRMs)
 +
|Yes
 +
|UCSC, ENSEMBL, Track Hub, IGV
 
|-
 
|-
 
|ChIPBase ([[http://rna.sysu.edu.cn/chipbase]])  
 
|ChIPBase ([[http://rna.sysu.edu.cn/chipbase]])  

Revision as of 17:35, 24 November 2017

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 v17.04 ([[1]]) GEO, SRA, ENCODE total 8828 human 4852 mouse 3916 rat 60 610 human and 373 mouse sequence specific TFs, corresponding to 713 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.

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