Difference between revisions of "GTRD comparison"

From BioUML platform
Jump to: navigation, search
(Created page with " {| border="1" |- !Database, URL !Source of human and mouse data !Number of samples (TF-related)* !Number of TFs !Number of ChIP-seq peak callers used !Metaclus-ter appro...")
 
 
(16 intermediate revisions by 3 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
+
!Metaclus-ter approach
+
!Uniform data processing
+
!Genome browser
+
 
|-
 
|-
|ChIPBase ([[http://rna.sysu.edu.cn/chipbase]])
+
| 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, 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/#/]])
+
| Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || 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]])
+
| 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
|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]])
+
| ENCODE || total: 3609* <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No
|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  
+
 
|-
 
|-
|GTRD ([[http://gtrd.biouml.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
|GEO, SRA, ENCODE
+
|total 5078 human 2955 mouse 2107 rat 16
+
|476 human and 257 mouse sequence specific TFs, corresponding to 542 TFClass classes.  
+
|4 (MACS, SISSRs, GEM, PICS)
+
|Yes
+
|Yes
+
|Self-developed
+
 
|-
 
|-
|ChIP-Atlas ([[http://chip-atlas.org]])
+
| ReMap 2018 v1.2 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <i>H. sapiens</i> || MACS2 || Yes (CRMs)
|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]])
+
| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No
|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).
 +
<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.

Personal tools
Namespaces

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