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Coexpression cluster:C2107: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002199!1.78e-12!46;UBERON:0002416!1.78e-12!46;UBERON:0010314!2.63e-12!132;UBERON:0003102!1.74e-11!99;UBERON:0007524!2.04e-10!73;UBERON:0002097!4.31e-10!41;UBERON:0003077!5.92e-10!72;UBERON:0007285!5.92e-10!72;UBERON:0002329!1.34e-09!71;UBERON:0003059!1.34e-09!71;UBERON:0007282!1.34e-09!71;UBERON:0004290!1.34e-09!71;UBERON:0009618!1.34e-09!71;UBERON:0002385!7.89e-09!64;UBERON:0001015!7.89e-09!64;UBERON:0000383!7.89e-09!64;UBERON:0000486!8.97e-09!83;UBERON:0001134!2.81e-08!62;UBERON:0002036!2.81e-08!62;UBERON:0003082!2.81e-08!62;UBERON:0000481!1.11e-07!342;UBERON:0003075!1.45e-07!82;UBERON:0007284!1.45e-07!82;UBERON:0007503!1.63e-07!78;UBERON:0004121!4.08e-07!171;UBERON:0000924!4.08e-07!171;UBERON:0006601!4.08e-07!171;UBERON:0000468!4.73e-07!656;UBERON:0010371!5.77e-07!104
|ontology_enrichment_uberon=UBERON:0002199!1.78e-12!46;UBERON:0002416!1.78e-12!46;UBERON:0010314!2.63e-12!132;UBERON:0003102!1.74e-11!99;UBERON:0007524!2.04e-10!73;UBERON:0002097!4.31e-10!41;UBERON:0003077!5.92e-10!72;UBERON:0007285!5.92e-10!72;UBERON:0002329!1.34e-09!71;UBERON:0003059!1.34e-09!71;UBERON:0007282!1.34e-09!71;UBERON:0004290!1.34e-09!71;UBERON:0009618!1.34e-09!71;UBERON:0002385!7.89e-09!64;UBERON:0001015!7.89e-09!64;UBERON:0000383!7.89e-09!64;UBERON:0000486!8.97e-09!83;UBERON:0001134!2.81e-08!62;UBERON:0002036!2.81e-08!62;UBERON:0003082!2.81e-08!62;UBERON:0000481!1.11e-07!342;UBERON:0003075!1.45e-07!82;UBERON:0007284!1.45e-07!82;UBERON:0007503!1.63e-07!78;UBERON:0004121!4.08e-07!171;UBERON:0000924!4.08e-07!171;UBERON:0006601!4.08e-07!171;UBERON:0000468!4.73e-07!656;UBERON:0010371!5.77e-07!104
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}}
}}

Revision as of 15:18, 26 November 2012


Full id: C2107_Fibroblast_Preadipocyte_mesenchymal_Chondrocyte_glioblastoma_Saos2_Smooth



Phase1 CAGE Peaks

Hg19::chr11:121972870..121972938,-p5@MIR100HG
Hg19::chr15:33021589..33021598,+p@chr15:33021589..33021598
+
Hg19::chr1:240726634..240726648,-p@chr1:240726634..240726648
-
Hg19::chr3:194090463..194090479,-p1@LRRC15


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
integument1.78e-1246
integumental system1.78e-1246
structure with developmental contribution from neural crest2.63e-12132
surface structure1.74e-1199
dense mesenchyme tissue2.04e-1073
skin of body4.31e-1041
paraxial mesoderm5.92e-1072
presumptive paraxial mesoderm5.92e-1072
somite1.34e-0971
presomitic mesoderm1.34e-0971
presumptive segmental plate1.34e-0971
dermomyotome1.34e-0971
trunk paraxial mesoderm1.34e-0971
muscle tissue7.89e-0964
musculature7.89e-0964
musculature of body7.89e-0964
multilaminar epithelium8.97e-0983
skeletal muscle tissue2.81e-0862
striated muscle tissue2.81e-0862
myotome2.81e-0862
multi-tissue structure1.11e-07342
neural plate1.45e-0782
presumptive neural plate1.45e-0782
epithelial vesicle1.63e-0778
ectoderm-derived structure4.08e-07171
ectoderm4.08e-07171
presumptive ectoderm4.08e-07171
multi-cellular organism4.73e-07656
ecto-epithelium5.77e-07104
Disease
Ontology termp-valuen
ovarian cancer5.35e-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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