Personal tools

Coexpression cluster:C328

From FANTOM5_SSTAR

Revision as of 13:44, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C328_Endothelial_Lymphatic_Renal_Hepatic_chronic_extraskeletal_adipose



Phase1 CAGE Peaks

Hg19::chr10:3477893..3477912,-p@chr10:3477893..3477912
-
Hg19::chr12:105863737..105863745,+p@chr12:105863737..105863745
+
Hg19::chr12:105882068..105882076,+p@chr12:105882068..105882076
+
Hg19::chr12:105889859..105889862,+p@chr12:105889859..105889862
+
Hg19::chr12:10794718..10794741,+p@chr12:10794718..10794741
+
Hg19::chr12:6232421..6232447,-p8@VWF
Hg19::chr12:6233700..6233715,-p2@VWF
Hg19::chr12:6233743..6233756,-p3@VWF
Hg19::chr12:71031305..71031308,-p20@PTPRB
Hg19::chr16:77468905..77468944,-p1@ADAMTS18
Hg19::chr16:82029551..82029560,+p@chr16:82029551..82029560
+
Hg19::chr1:65344781..65344820,-p3@JAK1
Hg19::chr21:39875736..39875750,+p@chr21:39875736..39875750
+
Hg19::chr3:149051346..149051364,-p3@TM4SF18
Hg19::chr3:149051376..149051400,-p1@TM4SF18
Hg19::chr3:149051406..149051430,-p2@TM4SF18
Hg19::chr3:149051444..149051476,-p4@TM4SF18
Hg19::chr4:90815997..90816012,+p1@MMRN1
Hg19::chr4:90816021..90816032,+p3@MMRN1
Hg19::chr4:90816033..90816048,+p2@MMRN1
Hg19::chr4:90857427..90857438,+p@chr4:90857427..90857438
+
Hg19::chr6:136358591..136358656,+p@chr6:136358591..136358656
+
Hg19::chr6:136358786..136358809,+p12@PDE7B
Hg19::chr6:136359549..136359565,+p2@AB384352
Hg19::chr6:136359569..136359580,+p3@AB384352
Hg19::chr6:3753188..3753192,-p@chr6:3753188..3753192
-
Hg19::chr6:79315735..79315760,-p1@ENST00000449463
Hg19::chr7:47988045..47988072,-p1@PKD1L1
Hg19::chr8:6420647..6420659,-p3@ANGPT2
Hg19::chr8:6420759..6420775,-p1@ANGPT2
Hg19::chr8:6420777..6420779,-p5@ANGPT2
Hg19::chr8:6420791..6420805,-p2@ANGPT2
Hg19::chr8:6420948..6420957,-p4@ANGPT2
Hg19::chr8:6459787..6459796,+p@chr8:6459787..6459796
+
Hg19::chrX:20236970..20237027,-p4@RPS6KA3


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0033093Weibel-Palade body0.015989329581669
GO:0007596blood coagulation0.015989329581669
GO:0050817coagulation0.015989329581669
GO:0007599hemostasis0.015989329581669
GO:0031091platelet alpha granule0.015989329581669
GO:0050878regulation of body fluid levels0.015989329581669
GO:0042060wound healing0.015989329581669
GO:0002020protease binding0.0224932504301092
GO:0005131growth hormone receptor binding0.0224932504301092
GO:0004718Janus kinase activity0.0253015549427426
GO:0001948glycoprotein binding0.0266751123096811
GO:0044421extracellular region part0.0266751123096811
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0266751123096811
GO:0022610biological adhesion0.0266751123096811
GO:0007155cell adhesion0.0266751123096811
GO:0032501multicellular organismal process0.0293181393445014
GO:0005102receptor binding0.0293181393445014
GO:0004716receptor signaling protein tyrosine kinase activity0.0365079860188144
GO:0051087chaperone binding0.0404235519267515
GO:0019865immunoglobulin binding0.0404235519267515
GO:0019198transmembrane receptor protein phosphatase activity0.041725131879665
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.041725131879665
GO:0005518collagen binding0.041725131879665
GO:0005578proteinaceous extracellular matrix0.0448232066429677
GO:0009611response to wounding0.0448232066429677
GO:0030168platelet activation0.0485281336967221



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism8.74e-45115
tube2.92e-26194
anatomical cluster1.36e-25286
anatomical conduit4.11e-24241
circulatory system4.75e-20113
neural tube2.42e-1957
neural rod2.42e-1957
future spinal cord2.42e-1957
neural keel2.42e-1957
regional part of brain6.59e-1959
cardiovascular system7.36e-19110
neural plate1.21e-1786
presumptive neural plate1.21e-1786
neurectoderm2.28e-1790
central nervous system2.46e-1782
regional part of nervous system9.69e-1794
nervous system9.69e-1794
brain1.07e-1669
future brain1.07e-1669
vasculature1.34e-1679
vascular system1.34e-1679
cell layer1.42e-16312
epithelium6.02e-16309
splanchnic layer of lateral plate mesoderm1.72e-1584
vessel3.18e-1569
anterior neural tube1.40e-1442
regional part of forebrain5.06e-1441
forebrain5.06e-1441
future forebrain5.06e-1441
blood vessel2.50e-1360
epithelial tube open at both ends2.50e-1360
blood vasculature2.50e-1360
vascular cord2.50e-1360
epithelial tube3.22e-13118
endothelium3.85e-1318
blood vessel endothelium3.85e-1318
cardiovascular system endothelium3.85e-1318
pre-chordal neural plate2.64e-1261
gray matter6.71e-1234
brain grey matter6.71e-1234
telencephalon1.53e-1134
regional part of telencephalon2.91e-1133
simple squamous epithelium2.96e-1122
anterior region of body3.57e-11129
craniocervical region3.57e-11129
squamous epithelium6.89e-1125
multi-cellular organism8.04e-11659
cerebral hemisphere8.88e-1132
head1.03e-10123
anatomical system1.31e-09625
multi-tissue structure1.77e-09347
anatomical group1.96e-09626
regional part of cerebral cortex2.10e-0822
cerebral cortex2.97e-0825
pallium2.97e-0825
ectoderm7.52e-08173
presumptive ectoderm7.52e-08173
ectoderm-derived structure8.64e-08169
neocortex1.28e-0720
primary circulatory organ2.53e-0727
endothelial tube3.04e-079
arterial system endothelium3.04e-079
endothelium of artery3.04e-079
artery3.30e-0742
arterial blood vessel3.30e-0742
arterial system3.30e-0742
organism subdivision5.51e-07365
embryo8.76e-07612


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235392.313759936572850.01234312400347420.044717064236119
GATA2#2624238.375240853478341.2167644793407e-172.60405052167752e-15
JUN#372593.217584649457910.001376091326126830.0089655397385752



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.