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Coexpression cluster:C1636: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1636_Mesenchymal_Alveolar_Placental_Smooth_Fibroblast_Bronchial_Hair
|full_id=C1636_Mesenchymal_Alveolar_Placental_Smooth_Fibroblast_Bronchial_Hair
|gostat_on_coexpression_clusters=GO:0032311!angiogenin-PRI complex!0.0126567374393484!6050$GO:0004045!aminoacyl-tRNA hydrolase activity!0.0126567374393484!138428$GO:0008428!ribonuclease inhibitor activity!0.0126567374393484!6050$GO:0030128!clathrin coat of endocytic vesicle!0.0151827206402137!1175$GO:0030669!clathrin-coated endocytic vesicle membrane!0.0151827206402137!1175$GO:0030122!AP-2 adaptor complex!0.0151827206402137!1175$GO:0030666!endocytic vesicle membrane!0.0151827206402137!1175$GO:0045334!clathrin-coated endocytic vesicle!0.0151827206402137!1175$GO:0006901!vesicle coating!0.0151827206402137!1175$GO:0048268!clathrin cage assembly!0.0151827206402137!1175$GO:0006900!membrane budding!0.0155268682942639!1175$GO:0030132!clathrin coat of coated pit!0.0205538827115248!1175$GO:0016050!vesicle organization and biogenesis!0.023347032623047!1175$GO:0030125!clathrin vesicle coat!0.0272573686613283!1175$GO:0030139!endocytic vesicle!0.0272573686613283!1175$GO:0030665!clathrin coated vesicle membrane!0.0272573686613283!1175$GO:0006402!mRNA catabolic process!0.0323349158877492!6050$GO:0030100!regulation of endocytosis!0.0357932574808114!1175$GO:0045765!regulation of angiogenesis!0.037889819044312!6050$GO:0005905!coated pit!0.0407195667967789!1175$GO:0006401!RNA catabolic process!0.040882474854515!6050$GO:0030120!vesicle coat!0.040882474854515!1175$GO:0030662!coated vesicle membrane!0.040882474854515!1175$GO:0030131!clathrin adaptor complex!0.040882474854515!1175$GO:0030119!AP-type membrane coat adaptor complex!0.040882474854515!1175$GO:0030118!clathrin coat!0.0480117110439507!1175
|gostat_on_coexpression_clusters=GO:0032311!angiogenin-PRI complex!0.0126567374393484!6050$GO:0004045!aminoacyl-tRNA hydrolase activity!0.0126567374393484!138428$GO:0008428!ribonuclease inhibitor activity!0.0126567374393484!6050$GO:0030128!clathrin coat of endocytic vesicle!0.0151827206402137!1175$GO:0030669!clathrin-coated endocytic vesicle membrane!0.0151827206402137!1175$GO:0030122!AP-2 adaptor complex!0.0151827206402137!1175$GO:0030666!endocytic vesicle membrane!0.0151827206402137!1175$GO:0045334!clathrin-coated endocytic vesicle!0.0151827206402137!1175$GO:0006901!vesicle coating!0.0151827206402137!1175$GO:0048268!clathrin cage assembly!0.0151827206402137!1175$GO:0006900!membrane budding!0.0155268682942639!1175$GO:0030132!clathrin coat of coated pit!0.0205538827115248!1175$GO:0016050!vesicle organization and biogenesis!0.023347032623047!1175$GO:0030125!clathrin vesicle coat!0.0272573686613283!1175$GO:0030139!endocytic vesicle!0.0272573686613283!1175$GO:0030665!clathrin coated vesicle membrane!0.0272573686613283!1175$GO:0006402!mRNA catabolic process!0.0323349158877492!6050$GO:0030100!regulation of endocytosis!0.0357932574808114!1175$GO:0045765!regulation of angiogenesis!0.037889819044312!6050$GO:0005905!coated pit!0.0407195667967789!1175$GO:0006401!RNA catabolic process!0.040882474854515!6050$GO:0030120!vesicle coat!0.040882474854515!1175$GO:0030662!coated vesicle membrane!0.040882474854515!1175$GO:0030131!clathrin adaptor complex!0.040882474854515!1175$GO:0030119!AP-type membrane coat adaptor complex!0.040882474854515!1175$GO:0030118!clathrin coat!0.0480117110439507!1175

Revision as of 14:13, 12 September 2012


Full id: C1636_Mesenchymal_Alveolar_Placental_Smooth_Fibroblast_Bronchial_Hair



Phase1 CAGE Peaks

Hg19::chr11:507184..507269,-p1@RNH1
Hg19::chr17:1945301..1945344,+p1@OVCA2
Hg19::chr19:47354082..47354132,-p1@AP2S1
Hg19::chr22:50963976..50964055,-p1@SCO2
Hg19::chr9:130477912..130477961,-p1@PTRH1


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:0032311angiogenin-PRI complex0.0126567374393484
GO:0004045aminoacyl-tRNA hydrolase activity0.0126567374393484
GO:0008428ribonuclease inhibitor activity0.0126567374393484
GO:0030128clathrin coat of endocytic vesicle0.0151827206402137
GO:0030669clathrin-coated endocytic vesicle membrane0.0151827206402137
GO:0030122AP-2 adaptor complex0.0151827206402137
GO:0030666endocytic vesicle membrane0.0151827206402137
GO:0045334clathrin-coated endocytic vesicle0.0151827206402137
GO:0006901vesicle coating0.0151827206402137
GO:0048268clathrin cage assembly0.0151827206402137
GO:0006900membrane budding0.0155268682942639
GO:0030132clathrin coat of coated pit0.0205538827115248
GO:0016050vesicle organization and biogenesis0.023347032623047
GO:0030125clathrin vesicle coat0.0272573686613283
GO:0030139endocytic vesicle0.0272573686613283
GO:0030665clathrin coated vesicle membrane0.0272573686613283
GO:0006402mRNA catabolic process0.0323349158877492
GO:0030100regulation of endocytosis0.0357932574808114
GO:0045765regulation of angiogenesis0.037889819044312
GO:0005905coated pit0.0407195667967789
GO:0006401RNA catabolic process0.040882474854515
GO:0030120vesicle coat0.040882474854515
GO:0030662coated vesicle membrane0.040882474854515
GO:0030131clathrin adaptor complex0.040882474854515
GO:0030119AP-type membrane coat adaptor complex0.040882474854515
GO:0030118clathrin coat0.0480117110439507



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>

Cell Type
Ontology termp-valuen
mesodermal cell7.71e-29119
embryonic cell8.22e-28248
animal cell1.50e-27679
eukaryotic cell1.50e-27679
somatic cell3.74e-27591
non-terminally differentiated cell3.04e-23180
contractile cell7.63e-2059
muscle precursor cell7.73e-1857
myoblast7.73e-1857
multi-potent skeletal muscle stem cell7.73e-1857
muscle cell3.87e-1754
native cell5.46e-16722
smooth muscle cell1.10e-1542
smooth muscle myoblast1.10e-1542
electrically responsive cell9.07e-1560
electrically active cell9.07e-1560
epithelial cell3.80e-14254
vascular associated smooth muscle cell3.46e-1332
endothelial cell4.11e-1135
meso-epithelial cell4.41e-1144
lining cell6.83e-1157
barrier cell6.83e-1157
fibroblast1.15e-0975
epithelial cell of nephron5.51e-0816
endothelial cell of vascular tree7.50e-0824
blood vessel endothelial cell9.76e-0818
embryonic blood vessel endothelial progenitor cell9.76e-0818
kidney cortical cell5.84e-0713
renal cortical epithelial cell5.84e-0713
Uber Anatomy
Ontology termp-valuen
vasculature1.37e-1979
vascular system1.37e-1979
epithelial tube1.41e-19118
somite1.54e-1983
paraxial mesoderm1.54e-1983
presomitic mesoderm1.54e-1983
presumptive segmental plate1.54e-1983
trunk paraxial mesoderm1.54e-1983
presumptive paraxial mesoderm1.54e-1983
multilaminar epithelium4.95e-1982
trunk mesenchyme5.00e-19143
dermomyotome1.63e-1870
splanchnic layer of lateral plate mesoderm3.79e-1884
vessel7.32e-1869
blood vessel1.02e-1660
epithelial tube open at both ends1.02e-1660
blood vasculature1.02e-1660
vascular cord1.02e-1660
unilaminar epithelium1.54e-16138
trunk1.83e-16216
artery1.04e-1542
arterial blood vessel1.04e-1542
arterial system1.04e-1542
skeletal muscle tissue2.01e-1561
striated muscle tissue2.01e-1561
myotome2.01e-1561
mesenchyme8.98e-15238
entire embryonic mesenchyme8.98e-15238
muscle tissue2.55e-1463
musculature2.55e-1463
musculature of body2.55e-1463
circulatory system2.07e-13113
cardiovascular system3.14e-13110
mesoderm8.53e-12448
mesoderm-derived structure8.53e-12448
presumptive mesoderm8.53e-12448
systemic artery1.78e-1133
systemic arterial system1.78e-1133
nephron epithelium5.51e-0816
nephron5.51e-0816
uriniferous tubule5.51e-0816
metanephric mesenchyme5.51e-0816
nephrogenic mesenchyme5.51e-0816
cell layer6.13e-08312
endothelium9.76e-0818
blood vessel endothelium9.76e-0818
cardiovascular system endothelium9.76e-0818
epithelium9.82e-08309
multi-tissue structure1.24e-07347
parenchyma1.35e-0717
excretory tube1.94e-0717
mesonephric epithelium1.94e-0717
mesonephric tubule1.94e-0717
nephric duct1.94e-0717
kidney epithelium1.94e-0717
renal duct1.94e-0717
mesonephric duct1.94e-0717
pronephric duct1.94e-0717
simple squamous epithelium2.48e-0722
squamous epithelium5.61e-0725
cortex of kidney5.84e-0713
renal parenchyma5.84e-0713
organism subdivision6.42e-07365


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
BRF2#552901214.915116279070.004644397888135530.0219254292383034
CHD2#110636.206413700470110.007774550126275590.0319457937851869
E2F1#186954.907389214879320.0003512818099256460.00352188931043722
EGR1#195843.990543275848110.0067800983001440.0287567692644874
ELF1#199743.406478367046030.01235066105299550.0447242013007106
ELK4#200539.741408995080820.00212558656574340.0122859115246929
ESR1#2099318.46116197769270.000326633459097560.00333007339268744
ETS1#211335.83725655332140.009253279045631430.0349652017166577
GABPB1#255345.654147068945740.001776696502096670.0109041785263251
IRF1#365957.63716375356393.84754333311872e-050.000723372777979454
MXI1#460135.976942977255580.008653004889366880.0329400830195221
MYC#460944.177825497287520.005691969036823440.0256687920133341
PBX3#5090313.14870761204650.0008860469322808430.00660135936370945
POU2F2#545235.463674434645510.01115650094469780.0410012598410616
SIN3A#2594244.327107781452110.004977052855762880.023237445715187
SIX5#147912310.25202921327540.001832291068677690.0108476076708593
SP1#666744.558705102512720.00407573565781680.0194759222349345
TAF1#687253.343046285745290.002394600090870310.0135154366023781
USF1#739156.361499277207969.59569864925045e-050.00136721032909832
YY1#752843.928936599883080.007193866269917620.0298320507986471
ZNF143#770238.100525931336740.003624870512090980.0183268553716546



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.

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