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Coexpression cluster:C3897: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001637!1.75e-21!42;UBERON:0003509!1.75e-21!42;UBERON:0004572!1.75e-21!42;UBERON:0000025!1.57e-19!192;UBERON:0004573!1.29e-18!33;UBERON:0004571!1.29e-18!33;UBERON:0010314!2.49e-17!132;UBERON:0001049!5.28e-17!56;UBERON:0005068!5.28e-17!56;UBERON:0006241!5.28e-17!56;UBERON:0007135!5.28e-17!56;UBERON:0007500!1.34e-16!59;UBERON:0001981!1.34e-16!59;UBERON:0004537!1.34e-16!59;UBERON:0006965!1.34e-16!59;UBERON:0000955!1.76e-16!68;UBERON:0006238!1.76e-16!68;UBERON:0000119!3.59e-16!309;UBERON:0000073!3.68e-16!53;UBERON:0002616!3.68e-16!53;UBERON:0001016!8.10e-16!89;UBERON:0002049!9.51e-16!78;UBERON:0007798!9.51e-16!78;UBERON:0004872!9.88e-16!83;UBERON:0000483!1.19e-15!306;UBERON:0001017!2.11e-15!81;UBERON:0003075!2.18e-15!82;UBERON:0007284!2.18e-15!82;UBERON:0001134!3.76e-15!62;UBERON:0002036!3.76e-15!62;UBERON:0003082!3.76e-15!62;UBERON:0002385!5.55e-15!64;UBERON:0001015!5.55e-15!64;UBERON:0000383!5.55e-15!64;UBERON:0003077!8.49e-15!72;UBERON:0007285!8.49e-15!72;UBERON:0004111!1.26e-14!240;UBERON:0007524!2.34e-14!73;UBERON:0002329!3.55e-14!71;UBERON:0003059!3.55e-14!71;UBERON:0007282!3.55e-14!71;UBERON:0004290!3.55e-14!71;UBERON:0009618!3.55e-14!71;UBERON:0002780!5.15e-14!41;UBERON:0001890!5.15e-14!41;UBERON:0003080!5.15e-14!41;UBERON:0006240!5.15e-14!41;UBERON:0007503!6.10e-14!78;UBERON:0000055!8.24e-14!68;UBERON:0002346!8.33e-14!86;UBERON:0001869!4.80e-13!32;UBERON:0000477!5.90e-13!373;UBERON:0002619!9.67e-13!22;UBERON:0001893!1.32e-12!34;UBERON:0003528!1.63e-12!34;UBERON:0002020!1.63e-12!34;UBERON:0004535!4.70e-12!109;UBERON:0000481!8.19e-12!342;UBERON:0002791!1.43e-11!32;UBERON:0001950!1.51e-11!20;UBERON:0003056!2.77e-11!61;UBERON:0001009!3.29e-11!112;UBERON:0000956!2.40e-10!25;UBERON:0000203!2.40e-10!25;UBERON:0010371!6.14e-10!104;UBERON:0000486!8.05e-10!83;UBERON:0000947!8.94e-10!21;UBERON:0010191!8.94e-10!21;UBERON:0003914!2.49e-09!117;UBERON:0005256!1.62e-08!122;UBERON:0000490!3.77e-08!148;UBERON:0007023!6.64e-08!114;UBERON:0000467!7.08e-08!624;UBERON:0000468!8.30e-08!656;UBERON:0000480!9.01e-08!625;UBERON:0004121!1.53e-07!171;UBERON:0000924!1.53e-07!171;UBERON:0006601!1.53e-07!171;UBERON:0003104!1.81e-07!160;UBERON:0009142!1.81e-07!160;UBERON:0002050!3.67e-07!564;UBERON:0000200!7.92e-07!6;UBERON:0004237!7.96e-07!10;UBERON:0004695!7.96e-07!10;UBERON:0002111!7.96e-07!10;UBERON:0004178!7.96e-07!10
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}}
}}

Revision as of 16:25, 26 November 2012


Full id: C3897_Mesothelial_Multipotent_mesenchymal_Fibroblast_argyrophil_medial_leiomyoma



Phase1 CAGE Peaks

Hg19::chr1:163038648..163038667,+p3@RGS4
Hg19::chr1:163038669..163038763,+p2@RGS4
Hg19::chr1:163039143..163039159,+p1@RGS4


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
artery1.75e-2142
arterial blood vessel1.75e-2142
arterial system1.75e-2142
tube1.57e-19192
systemic artery1.29e-1833
systemic arterial system1.29e-1833
structure with developmental contribution from neural crest2.49e-17132
neural tube5.28e-1756
neural rod5.28e-1756
future spinal cord5.28e-1756
neural keel5.28e-1756
epithelial tube open at both ends1.34e-1659
blood vessel1.34e-1659
blood vasculature1.34e-1659
vascular cord1.34e-1659
brain1.76e-1668
future brain1.76e-1668
cell layer3.59e-16309
regional part of nervous system3.68e-1653
regional part of brain3.68e-1653
nervous system8.10e-1689
vasculature9.51e-1678
vascular system9.51e-1678
splanchnic layer of lateral plate mesoderm9.88e-1683
epithelium1.19e-15306
central nervous system2.11e-1581
neural plate2.18e-1582
presumptive neural plate2.18e-1582
skeletal muscle tissue3.76e-1562
striated muscle tissue3.76e-1562
myotome3.76e-1562
muscle tissue5.55e-1564
musculature5.55e-1564
musculature of body5.55e-1564
paraxial mesoderm8.49e-1572
presumptive paraxial mesoderm8.49e-1572
anatomical conduit1.26e-14240
dense mesenchyme tissue2.34e-1473
somite3.55e-1471
presomitic mesoderm3.55e-1471
presumptive segmental plate3.55e-1471
dermomyotome3.55e-1471
trunk paraxial mesoderm3.55e-1471
regional part of forebrain5.15e-1441
forebrain5.15e-1441
anterior neural tube5.15e-1441
future forebrain5.15e-1441
epithelial vesicle6.10e-1478
vessel8.24e-1468
neurectoderm8.33e-1486
cerebral hemisphere4.80e-1332
anatomical cluster5.90e-13373
regional part of cerebral cortex9.67e-1322
telencephalon1.32e-1234
brain grey matter1.63e-1234
gray matter1.63e-1234
cardiovascular system4.70e-12109
multi-tissue structure8.19e-12342
regional part of telencephalon1.43e-1132
neocortex1.51e-1120
pre-chordal neural plate2.77e-1161
circulatory system3.29e-11112
cerebral cortex2.40e-1025
pallium2.40e-1025
ecto-epithelium6.14e-10104
multilaminar epithelium8.05e-1083
aorta8.94e-1021
aortic system8.94e-1021
epithelial tube2.49e-09117
trunk mesenchyme1.62e-08122
unilaminar epithelium3.77e-08148
adult organism6.64e-08114
anatomical system7.08e-08624
multi-cellular organism8.30e-08656
anatomical group9.01e-08625
ectoderm-derived structure1.53e-07171
ectoderm1.53e-07171
presumptive ectoderm1.53e-07171
mesenchyme1.81e-07160
entire embryonic mesenchyme1.81e-07160
embryonic structure3.67e-07564
gyrus7.92e-076
blood vessel smooth muscle7.96e-0710
arterial system smooth muscle7.96e-0710
artery smooth muscle tissue7.96e-0710
aorta smooth muscle tissue7.96e-0710

Disease
Ontology termp-valuen


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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