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Coexpression cluster:C3039: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!1.80e-34!79;UBERON:0007798!1.80e-34!79;UBERON:0000055!3.76e-28!69;UBERON:0001981!1.28e-26!60;UBERON:0007500!1.28e-26!60;UBERON:0004537!1.28e-26!60;UBERON:0006965!1.28e-26!60;UBERON:0004872!2.09e-26!84;UBERON:0004535!1.23e-25!110;UBERON:0001009!3.22e-25!113;UBERON:0003914!1.45e-24!118;UBERON:0001637!1.80e-22!42;UBERON:0003509!1.80e-22!42;UBERON:0004572!1.80e-22!42;UBERON:0000914!2.93e-21!83;UBERON:0002329!2.93e-21!83;UBERON:0003077!2.93e-21!83;UBERON:0003059!2.93e-21!83;UBERON:0007282!2.93e-21!83;UBERON:0009618!2.93e-21!83;UBERON:0007285!2.93e-21!83;UBERON:0000119!5.55e-21!312;UBERON:0004290!9.49e-21!70;UBERON:0000483!1.23e-19!309;UBERON:0004573!1.49e-18!33;UBERON:0004571!1.49e-18!33;UBERON:0001134!1.63e-18!61;UBERON:0002036!1.63e-18!61;UBERON:0003082!1.63e-18!61;UBERON:0000490!1.66e-18!138;UBERON:0005256!1.95e-18!143;UBERON:0002385!2.73e-18!63;UBERON:0001015!2.73e-18!63;UBERON:0000383!2.73e-18!63;UBERON:0000477!3.52e-18!286;UBERON:0000468!9.75e-18!659;UBERON:0004111!7.25e-17!241;UBERON:0000486!9.50e-17!82;UBERON:0000475!1.13e-15!365;UBERON:0000467!3.35e-14!625;UBERON:0000025!3.52e-14!194;UBERON:0000480!6.05e-14!626;UBERON:0002100!7.95e-14!216;UBERON:0000481!1.23e-13!347;UBERON:0000947!2.32e-12!21;UBERON:0010191!2.32e-12!21;UBERON:0000922!2.70e-10!612;UBERON:0000487!7.42e-10!22;UBERON:0002050!3.37e-09!605;UBERON:0005423!3.37e-09!605;UBERON:0001986!3.43e-09!18;UBERON:0004638!3.43e-09!18;UBERON:0004852!3.43e-09!18;UBERON:0003104!4.15e-09!238;UBERON:0009142!4.15e-09!238;UBERON:0000923!5.09e-09!604;UBERON:0005291!5.09e-09!604;UBERON:0006598!5.09e-09!604;UBERON:0002532!5.09e-09!604;UBERON:0006914!8.16e-09!25;UBERON:0000926!4.23e-07!448;UBERON:0004120!4.23e-07!448;UBERON:0006603!4.23e-07!448;UBERON:0000948!5.03e-07!24;UBERON:0005498!5.03e-07!24;UBERON:0004140!5.03e-07!24;UBERON:0009881!5.03e-07!24;UBERON:0004141!5.03e-07!24;UBERON:0003084!5.03e-07!24;UBERON:0007005!5.03e-07!24;UBERON:0004139!5.03e-07!24;UBERON:0004291!5.03e-07!24;UBERON:0004237!7.66e-07!10;UBERON:0004695!7.66e-07!10;UBERON:0002111!7.66e-07!10;UBERON:0004178!7.66e-07!10;UBERON:0003102!9.75e-07!95
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}}
}}

Revision as of 18:51, 8 August 2012


Full id: C3039_Pericytes_Smooth_alveolar_Fibroblast_fibrosarcoma_Lens_Meningeal



Phase1 CAGE Peaks

Hg19::chr10:71561630..71561641,+p3@COL13A1
Hg19::chr10:71561649..71561703,+p1@COL13A1
Hg19::chr10:71561704..71561747,+p2@COL13A1


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

No GOStat results

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
vasculature1.80e-3479
vascular system1.80e-3479
vessel3.76e-2869
blood vessel1.28e-2660
epithelial tube open at both ends1.28e-2660
blood vasculature1.28e-2660
vascular cord1.28e-2660
splanchnic layer of lateral plate mesoderm2.09e-2684
cardiovascular system1.23e-25110
circulatory system3.22e-25113
epithelial tube1.45e-24118
artery1.80e-2242
arterial blood vessel1.80e-2242
arterial system1.80e-2242
somite2.93e-2183
paraxial mesoderm2.93e-2183
presomitic mesoderm2.93e-2183
presumptive segmental plate2.93e-2183
trunk paraxial mesoderm2.93e-2183
presumptive paraxial mesoderm2.93e-2183
cell layer5.55e-21312
dermomyotome9.49e-2170
epithelium1.23e-19309
systemic artery1.49e-1833
systemic arterial system1.49e-1833
skeletal muscle tissue1.63e-1861
striated muscle tissue1.63e-1861
myotome1.63e-1861
unilaminar epithelium1.66e-18138
trunk mesenchyme1.95e-18143
muscle tissue2.73e-1863
musculature2.73e-1863
musculature of body2.73e-1863
anatomical cluster3.52e-18286
multi-cellular organism9.75e-18659
anatomical conduit7.25e-17241
multilaminar epithelium9.50e-1782
organism subdivision1.13e-15365
anatomical system3.35e-14625
tube3.52e-14194
anatomical group6.05e-14626
trunk7.95e-14216
multi-tissue structure1.23e-13347
aorta2.32e-1221
aortic system2.32e-1221
embryo2.70e-10612
simple squamous epithelium7.42e-1022
embryonic structure3.37e-09605
developing anatomical structure3.37e-09605
endothelium3.43e-0918
blood vessel endothelium3.43e-0918
cardiovascular system endothelium3.43e-0918
mesenchyme4.15e-09238
entire embryonic mesenchyme4.15e-09238
germ layer5.09e-09604
embryonic tissue5.09e-09604
presumptive structure5.09e-09604
epiblast (generic)5.09e-09604
squamous epithelium8.16e-0925
mesoderm4.23e-07448
mesoderm-derived structure4.23e-07448
presumptive mesoderm4.23e-07448
heart5.03e-0724
primitive heart tube5.03e-0724
primary heart field5.03e-0724
anterior lateral plate mesoderm5.03e-0724
heart tube5.03e-0724
heart primordium5.03e-0724
cardiac mesoderm5.03e-0724
cardiogenic plate5.03e-0724
heart rudiment5.03e-0724
blood vessel smooth muscle7.66e-0710
arterial system smooth muscle7.66e-0710
artery smooth muscle tissue7.66e-0710


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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