Difference between revisions of "GTRD comparison"

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! Database !! Number of TF ChIP-seq samples <br/>!! Number of TFs !! Species !! ChIP-seq peak callers !! Metacluster approach
 
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!Database, URL
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| GTRD v19.10 || total: 30670* <br/> human: 13515* || total: 3376* <br/> human: 1339* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, 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: 22872* <br/> human: 10129* || total: 1972* <br/> human: 878* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || 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: 24065* <br/> human: 13976* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No
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|GEO, ENCODE, ARRAYEXPRESS
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|3549 human
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|486 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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| NGS-QC || total: 22398* <br/> human: 11597* || total: Unkonwn <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</i> || None || No
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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: 3609* <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || 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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|ENCODE ([[https://www.encodeproject.org]])
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| ChIPBase || total: 4300 <br/> human: 2498 || total: 870 <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> 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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| ReMap 2018 v1.2 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <i>H. sapiens</i> || MACS2 || Yes (CRMs)
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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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| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || 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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|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> TFs and others (without histone modifications).
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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.
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<br/><nowiki>**</nowiki> The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.

Latest revision as of 12:45, 8 November 2019

Database Number of TF ChIP-seq samples
Number of TFs Species ChIP-seq peak callers Metacluster approach
GTRD v19.10 total: 30670*
human: 13515* 		total: 3376*
human: 1339* 		H. sapiens, M. musculus, R. norvegicus,
D. melanogaster, C. elegans, D. rerio,
S. pombe, S. cerevisiae, A. thaliana 		MACS2, SISSRs, GEM, PICS Yes
ChIP-Atlas total: 22872*
human: 10129* 		total: 1972*
human: 878* 		H. sapiens, M. musculus, R. norvegicus,
D. melanogaster, C. elegans, S. cerevisiae 		MACS2 No
Cistrome DB total: 24065*
human: 13976* 		total: Unknown
human: Unknown 		H. sapiens, M. musculus MACS2 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
ENCODE total: 3609*
human: 2407 		total: Unknown
human: Unknown 		H. sapiens, M. musculus, D. melanogaster,
C. elegans 		SPP No
ChIPBase total: 4300
human: 2498 		total: 870
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
ReMap 2018 v1.2 total: 2829*
human: 2829* 		total: 485
human: 485 		H. sapiens MACS2 Yes (CRMs)
Factorbook total: 1007
human: 837 		total: 167
human: 51 		H. sapiens, M. musculus None No

* TFs and others (without histone modifications).
** The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.

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