Difference between revisions of "GTRD comparison"

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! Database !! Number of TF ChIP-seq samples ( * - and others ) !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach
 
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!Database, URL
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| GTRD v18.06 || total: 17485 <br/> human: 7239 || total: 2399 <br/> human: 852 || H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, D. rerio, S. pombe, S. cerevisiae, A. thaliana || MACS, SISSRs, GEM, PICS || Yes 
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!Source of human and mouse data
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!Number of samples (TF-related)*
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!Number of TFs
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!Number of ChIP-seq peak callers used
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!Metacluster approach
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!Uniform data processing
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!Genome browser
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|GTRD v18.01 ([[http://gtrd.biouml.org]])
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| ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No
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|GEO, SRA, ENCODE
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|total 10418, human 5603, mouse 4815
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|682 human and 384 mouse sequence specific TFs, corresponding to 766 TFClass classes.  
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|4 (MACS, SISSRs, GEM, PICS)
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|Yes
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|Yes
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|Self-developed
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|ReMap 2018 ([[http://remap.cisreg.eu]])
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| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || H. sapiens, M. musculus || MACS2 || No
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|GEO, ENCODE, ARRAYEXPRESS
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|2829 human
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|485 TFs and non-TFs
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|MACS2
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|Yes(CRMs)
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|Yes
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|UCSC, ENSEMBL, Track Hub, IGV
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|ChIPBase ([[http://rna.sysu.edu.cn/chipbase]])
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| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)
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|GEO, ENCODE
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|total 3549 human 2498 mouse 1036 rat 15
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|252 TFs and non-TFs for 10 species
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|&gt;10 in total, but no uniform pipeline, each ChIP-seq is processed by different peak caller
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|No
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|No
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|Self-developed: deepView genomeView
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|Cistrome DB ([[http://dc2.cistrome.org/#/]])
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| ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, C. elegans || SPP, GEM, PeakSeq, MACS || No
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|GEO, SRA, ENA, ENCODE
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|total 10 276 (TF+non-TF) human 5774 mouse 4502 rat 0
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|260 TFs and non-TFs
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|1 (MACS2)
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|No  
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|Yes
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|UCSC genome browser
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|-
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|ENCODE ([[https://www.encodeproject.org]])
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| ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> 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
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|ENCODE
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|total 1448 human 1254 mouse 194 rat 0
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|295 TFs and non-TFs for human, 52 TFs and non-TFs for mouse
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|5 (SPP, GEM, PeakSeq, MACS, Hotspot/Hotspot2)
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|No
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|Yes
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|Self-developed: UCSC genome browser and WashU epigenome browser
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|Factorbook ([[http://www.factorbook.org]])
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| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || H. sapiens, M. musculus || None || No
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|ENCODE
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|total 1007 human 837 mouse 170 rat 0
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|167 TFs, co-factors and chromatin remodeling factors for human, 51&mdash;for mouse
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|None
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|No
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|No
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|No  
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|-
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|ChIP-Atlas ([[http://chip-atlas.org]])
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| NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, D. rerio, C. elegans, D. melanogaster, S. cerevisiae, A. thaliana, G. gallus, P. troglodytes || None || No
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|SRA
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|total 10 774 human 5914 mouse 4860 rat 0
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|699 human and 502 mouse TFs and others.
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|1(MACS2)
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|No
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|Yes
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|IGV
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|-
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|GeneProf ([[http://www.geneprof.org]])
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|SRA, ENCODE, literature
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|total 1692 human 693 mouse 999 rat 0
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|133 human and 131 mouse TFs
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|1(MACS)
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|No
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|Yes
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|Self-developed: based on GenomeGraphs
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|-
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|NGS-QC ([[http://www.ngs-qc.org]])
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|GEO
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|total 6672 human 4234 mouse 2438 rat 0
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|unknown
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|None  
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|No
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|Yes
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|No  
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|}
 
|}
  
 
<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 14:30, 12 November 2018

Database Number of TF ChIP-seq samples ( * - and others ) Number of TF ( * - and others ) Species ChIP-seq peak callers Metacluster approach
GTRD v18.06 total: 17485
human: 7239 		total: 2399
human: 852 		H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, D. rerio, S. pombe, S. cerevisiae, A. thaliana MACS, 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, GEM, PeakSeq, MACS 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.

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