Difference between revisions of "GTRD comparison"

From BioUML platform
Jump to: navigation, search
 
(12 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
 
+
{| class="wikitable"
−
{| border="1"
+
! Database !! Number of TF ChIP-seq samples <br/>!! Number of TFs !! Species !! ChIP-seq peak callers !! Metacluster approach
 
|-
 
|-
−
!Database, URL
+
| 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 
−
!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 v17.11 ([[http://gtrd.biouml.org]])
+
| 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
−
|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 ([[http://remap.cisreg.eu]])
+
| Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No
−
|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]])
+
| 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
−
|GEO, ENCODE
+
−
|total 3549 human 2498 mouse 1036 rat 15
+
−
|252 TFs and non-TFs for 10 species
+
−
|&gt;10 in total, but no uniform pipeline, each ChIP-seq is processed by different peak caller
+
−
|No
+
−
|No
+
−
|Self-developed: deepView genomeView
+
 
|-
 
|-
−
|Cistrome DB ([[http://dc2.cistrome.org/#/]])
+
| ENCODE || total: 3609* <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No
−
|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 ([[https://www.encodeproject.org]])
+
| 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
−
|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 ([[http://www.factorbook.org]])
+
| ReMap 2018 v1.2 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <i>H. sapiens</i> || MACS2 || Yes (CRMs)
−
|ENCODE
+
−
|total 1007 human 837 mouse 170 rat 0
+
−
|167 TFs, co-factors and chromatin remodeling factors for human, 51&mdash;for mouse
+
−
|None
+
−
|No
+
−
|No
+
−
|No
+
 
|-
 
|-
−
|ChIP-Atlas ([[http://chip-atlas.org]])
+
| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No
−
|SRA
+
−
|total 10 774 human 5914 mouse 4860 rat 0
+
−
|699 human and 502 mouse TFs and others.
+
−
|1(MACS2)
+
−
|No
+
−
|Yes
+
−
|IGV
+
−
|-
+
−
|GeneProf ([[http://www.geneprof.org]])
+
−
|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 ([[http://www.ngs-qc.org]])
+
−
|GEO
+
−
|total 6672 human 4234 mouse 2438 rat 0
+
−
|unknown
+
−
|None  
+
−
|No
+
−
|Yes
+
−
|No  
+
 
|}
 
|}
−
 
+
<nowiki>*</nowiki> TFs and others (without histone modifications).
−
<nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.
+
<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.

Retrieved from "https://wiki.biouml.org/index.php?title=GTRD_comparison&oldid=8435"
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox