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Coexpression cluster:C2181: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007503!5.68e-22!78;UBERON:0002049!1.07e-21!78;UBERON:0007798!1.07e-21!78;UBERON:0000486!2.32e-20!83;UBERON:0000055!2.77e-20!68;UBERON:0003914!2.87e-20!117;UBERON:0002329!8.78e-20!71;UBERON:0003059!8.78e-20!71;UBERON:0007282!8.78e-20!71;UBERON:0004290!8.78e-20!71;UBERON:0009618!8.78e-20!71;UBERON:0007524!1.15e-19!73;UBERON:0005256!2.19e-19!122;UBERON:0004872!2.27e-19!83;UBERON:0003077!3.98e-19!72;UBERON:0007285!3.98e-19!72;UBERON:0001637!4.15e-19!42;UBERON:0003509!4.15e-19!42;UBERON:0004572!4.15e-19!42;UBERON:0000490!9.32e-19!148;UBERON:0007500!1.10e-18!59;UBERON:0001981!1.10e-18!59;UBERON:0004537!1.10e-18!59;UBERON:0006965!1.10e-18!59;UBERON:0001134!1.84e-18!62;UBERON:0002036!1.84e-18!62;UBERON:0003082!1.84e-18!62;UBERON:0003104!3.41e-18!160;UBERON:0009142!3.41e-18!160;UBERON:0002385!1.02e-17!64;UBERON:0001015!1.02e-17!64;UBERON:0000383!1.02e-17!64;UBERON:0004535!4.31e-17!109;UBERON:0001009!9.72e-17!112;UBERON:0000926!7.87e-16!315;UBERON:0004120!7.87e-16!315;UBERON:0006603!7.87e-16!315;UBERON:0004573!1.61e-15!33;UBERON:0004571!1.61e-15!33;UBERON:0000475!2.03e-13!264;UBERON:0002100!2.52e-13!199;UBERON:0000468!2.04e-12!656;UBERON:0000480!1.61e-11!625;UBERON:0000467!3.48e-11!624;UBERON:0000119!6.45e-09!309;UBERON:0000947!7.24e-09!21;UBERON:0010191!7.24e-09!21;UBERON:0000483!1.13e-08!306;UBERON:0002204!1.94e-08!167;UBERON:0003102!3.72e-07!99;UBERON:0003081!4.48e-07!203;UBERON:0000481!5.36e-07!342;UBERON:0005423!9.13e-07!581
|ontology_enrichment_uberon=UBERON:0007503!5.68e-22!78;UBERON:0002049!1.07e-21!78;UBERON:0007798!1.07e-21!78;UBERON:0000486!2.32e-20!83;UBERON:0000055!2.77e-20!68;UBERON:0003914!2.87e-20!117;UBERON:0002329!8.78e-20!71;UBERON:0003059!8.78e-20!71;UBERON:0007282!8.78e-20!71;UBERON:0004290!8.78e-20!71;UBERON:0009618!8.78e-20!71;UBERON:0007524!1.15e-19!73;UBERON:0005256!2.19e-19!122;UBERON:0004872!2.27e-19!83;UBERON:0003077!3.98e-19!72;UBERON:0007285!3.98e-19!72;UBERON:0001637!4.15e-19!42;UBERON:0003509!4.15e-19!42;UBERON:0004572!4.15e-19!42;UBERON:0000490!9.32e-19!148;UBERON:0007500!1.10e-18!59;UBERON:0001981!1.10e-18!59;UBERON:0004537!1.10e-18!59;UBERON:0006965!1.10e-18!59;UBERON:0001134!1.84e-18!62;UBERON:0002036!1.84e-18!62;UBERON:0003082!1.84e-18!62;UBERON:0003104!3.41e-18!160;UBERON:0009142!3.41e-18!160;UBERON:0002385!1.02e-17!64;UBERON:0001015!1.02e-17!64;UBERON:0000383!1.02e-17!64;UBERON:0004535!4.31e-17!109;UBERON:0001009!9.72e-17!112;UBERON:0000926!7.87e-16!315;UBERON:0004120!7.87e-16!315;UBERON:0006603!7.87e-16!315;UBERON:0004573!1.61e-15!33;UBERON:0004571!1.61e-15!33;UBERON:0000475!2.03e-13!264;UBERON:0002100!2.52e-13!199;UBERON:0000468!2.04e-12!656;UBERON:0000480!1.61e-11!625;UBERON:0000467!3.48e-11!624;UBERON:0000119!6.45e-09!309;UBERON:0000947!7.24e-09!21;UBERON:0010191!7.24e-09!21;UBERON:0000483!1.13e-08!306;UBERON:0002204!1.94e-08!167;UBERON:0003102!3.72e-07!99;UBERON:0003081!4.48e-07!203;UBERON:0000481!5.36e-07!342;UBERON:0005423!9.13e-07!581
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}}
}}

Revision as of 15:20, 26 November 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
mesodermal cell3.04e-25121
contractile cell6.87e-2159
muscle precursor cell8.50e-2158
myoblast8.50e-2158
multi-potent skeletal muscle stem cell8.50e-2158
fibroblast1.83e-2076
smooth muscle cell6.44e-2043
smooth muscle myoblast6.44e-2043
muscle cell7.30e-2055
somatic cell3.10e-19588
animal cell7.20e-17679
eukaryotic cell7.20e-17679
vascular associated smooth muscle cell9.78e-1732
electrically responsive cell2.10e-1561
electrically active cell2.10e-1561
embryonic cell6.36e-14250
non-terminally differentiated cell2.59e-13106
multi fate stem cell1.29e-10427
somatic stem cell4.91e-10433
stem cell6.26e-09441
native cell5.71e-08722
lining cell6.78e-0758
barrier cell6.78e-0758
skin fibroblast6.88e-0723
cardiocyte7.51e-0716
Uber Anatomy
Ontology termp-valuen
epithelial vesicle5.68e-2278
vasculature1.07e-2178
vascular system1.07e-2178
multilaminar epithelium2.32e-2083
vessel2.77e-2068
epithelial tube2.87e-20117
somite8.78e-2071
presomitic mesoderm8.78e-2071
presumptive segmental plate8.78e-2071
dermomyotome8.78e-2071
trunk paraxial mesoderm8.78e-2071
dense mesenchyme tissue1.15e-1973
trunk mesenchyme2.19e-19122
splanchnic layer of lateral plate mesoderm2.27e-1983
paraxial mesoderm3.98e-1972
presumptive paraxial mesoderm3.98e-1972
artery4.15e-1942
arterial blood vessel4.15e-1942
arterial system4.15e-1942
unilaminar epithelium9.32e-19148
epithelial tube open at both ends1.10e-1859
blood vessel1.10e-1859
blood vasculature1.10e-1859
vascular cord1.10e-1859
skeletal muscle tissue1.84e-1862
striated muscle tissue1.84e-1862
myotome1.84e-1862
mesenchyme3.41e-18160
entire embryonic mesenchyme3.41e-18160
muscle tissue1.02e-1764
musculature1.02e-1764
musculature of body1.02e-1764
cardiovascular system4.31e-17109
circulatory system9.72e-17112
mesoderm7.87e-16315
mesoderm-derived structure7.87e-16315
presumptive mesoderm7.87e-16315
systemic artery1.61e-1533
systemic arterial system1.61e-1533
organism subdivision2.03e-13264
trunk2.52e-13199
multi-cellular organism2.04e-12656
anatomical group1.61e-11625
anatomical system3.48e-11624
cell layer6.45e-09309
aorta7.24e-0921
aortic system7.24e-0921
epithelium1.13e-08306
musculoskeletal system1.94e-08167
surface structure3.72e-0799
lateral plate mesoderm4.48e-07203
multi-tissue structure5.36e-07342
developing anatomical structure9.13e-07581
Disease
Ontology termp-valuen
ovarian cancer4.69e-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)

{{{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

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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