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Coexpression cluster:C2181: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2181_Smooth_Fibroblast_leiomyoma_mesenchymal_hepatic_normal_Preadipocyte
|full_id=C2181_Smooth_Fibroblast_leiomyoma_mesenchymal_hepatic_normal_Preadipocyte
|gostat_on_coexpression_clusters=GO:0046922!peptide-O-fucosyltransferase activity!0.00400323791041627!23275$GO:0033116!ER-Golgi intermediate compartment membrane!0.0072041312773884!10970$GO:0005783!endoplasmic reticulum!0.0072041312773884!23275;10970$GO:0006004!fucose metabolic process!0.0072041312773884!23275$GO:0008417!fucosyltransferase activity!0.0072041312773884!23275$GO:0005793!ER-Golgi intermediate compartment!0.0143362791822346!10970
|gostat_on_coexpression_clusters=GO:0046922!peptide-O-fucosyltransferase activity!0.00400323791041627!23275$GO:0033116!ER-Golgi intermediate compartment membrane!0.0072041312773884!10970$GO:0005783!endoplasmic reticulum!0.0072041312773884!23275;10970$GO:0006004!fucose metabolic process!0.0072041312773884!23275$GO:0008417!fucosyltransferase activity!0.0072041312773884!23275$GO:0005793!ER-Golgi intermediate compartment!0.0143362791822346!10970

Revision as of 14:52, 12 September 2012


Full id: C2181_Smooth_Fibroblast_leiomyoma_mesenchymal_hepatic_normal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr12:106633037..106633066,-p10@CKAP4
Hg19::chr12:106641713..106641725,-p4@CKAP4
Hg19::chr12:106641728..106641805,-p1@CKAP4
Hg19::chr21:46707793..46707815,-p1@POFUT2


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:0046922peptide-O-fucosyltransferase activity0.00400323791041627
GO:0033116ER-Golgi intermediate compartment membrane0.0072041312773884
GO:0005783endoplasmic reticulum0.0072041312773884
GO:0006004fucose metabolic process0.0072041312773884
GO:0008417fucosyltransferase activity0.0072041312773884
GO:0005793ER-Golgi intermediate compartment0.0143362791822346



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>disease_data<br>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.43e-36180
mesodermal cell1.98e-25119
contractile cell1.07e-2159
muscle precursor cell2.34e-2157
myoblast2.34e-2157
multi-potent skeletal muscle stem cell2.34e-2157
muscle cell2.13e-2054
smooth muscle cell2.98e-2042
smooth muscle myoblast2.98e-2042
fibroblast8.74e-2075
somatic cell2.04e-19591
animal cell1.05e-18679
eukaryotic cell1.05e-18679
electrically responsive cell4.41e-1760
electrically active cell4.41e-1760
embryonic cell4.57e-17248
vascular associated smooth muscle cell4.90e-1732
multi fate stem cell3.23e-09430
somatic stem cell8.64e-09436
native cell6.46e-08722
stem cell8.32e-08444
cardiocyte3.30e-0716
skin fibroblast6.10e-0723
lining cell9.95e-0757
barrier cell9.95e-0757
Uber Anatomy
Ontology termp-valuen
vasculature2.31e-2279
vascular system2.31e-2279
somite1.43e-2183
paraxial mesoderm1.43e-2183
presomitic mesoderm1.43e-2183
presumptive segmental plate1.43e-2183
trunk paraxial mesoderm1.43e-2183
presumptive paraxial mesoderm1.43e-2183
multilaminar epithelium2.06e-2182
trunk mesenchyme2.37e-21143
vessel7.86e-2169
dermomyotome1.10e-2070
epithelial tube1.36e-20118
splanchnic layer of lateral plate mesoderm1.41e-2084
artery1.45e-1942
arterial blood vessel1.45e-1942
arterial system1.45e-1942
skeletal muscle tissue2.94e-1961
striated muscle tissue2.94e-1961
myotome2.94e-1961
blood vessel3.38e-1960
epithelial tube open at both ends3.38e-1960
blood vasculature3.38e-1960
vascular cord3.38e-1960
cardiovascular system5.67e-19110
circulatory system1.44e-18113
muscle tissue2.57e-1863
musculature2.57e-1863
musculature of body2.57e-1863
unilaminar epithelium6.06e-18138
mesoderm1.84e-16448
mesoderm-derived structure1.84e-16448
presumptive mesoderm1.84e-16448
trunk3.89e-16216
systemic artery1.05e-1533
systemic arterial system1.05e-1533
multi-cellular organism5.21e-15659
anatomical group8.54e-13626
anatomical system1.95e-12625
mesenchyme2.82e-11238
entire embryonic mesenchyme2.82e-11238
aorta8.26e-0921
aortic system8.26e-0921
organism subdivision1.84e-08365
musculoskeletal system2.77e-08167
embryonic structure2.89e-08605
developing anatomical structure2.89e-08605
embryo3.97e-08612
germ layer4.10e-08604
embryonic tissue4.10e-08604
presumptive structure4.10e-08604
epiblast (generic)4.10e-08604
cell layer5.15e-08312
lateral plate mesoderm8.14e-08216
epithelium8.24e-08309
surface structure9.89e-0895
Disease
Ontology termp-valuen
ovarian cancer2.69e-0714


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)

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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

No analysis results for this cluster

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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