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Coexpression cluster:C1719: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!1.21e-15!114;UBERON:0002097!8.11e-14!41;UBERON:0002199!6.10e-12!46;UBERON:0002416!6.10e-12!46;UBERON:0003075!5.00e-09!82;UBERON:0007284!5.00e-09!82;UBERON:0001049!1.12e-08!56;UBERON:0005068!1.12e-08!56;UBERON:0006241!1.12e-08!56;UBERON:0007135!1.12e-08!56;UBERON:0001893!1.94e-08!34;UBERON:0002346!2.03e-08!86;UBERON:0002780!5.00e-08!41;UBERON:0001890!5.00e-08!41;UBERON:0003080!5.00e-08!41;UBERON:0006240!5.00e-08!41;UBERON:0000073!5.31e-08!53;UBERON:0002616!5.31e-08!53;UBERON:0010371!3.24e-07!104;UBERON:0003528!5.50e-07!34;UBERON:0002020!5.50e-07!34
|ontology_enrichment_uberon=UBERON:0007023!1.21e-15!114;UBERON:0002097!8.11e-14!41;UBERON:0002199!6.10e-12!46;UBERON:0002416!6.10e-12!46;UBERON:0003075!5.00e-09!82;UBERON:0007284!5.00e-09!82;UBERON:0001049!1.12e-08!56;UBERON:0005068!1.12e-08!56;UBERON:0006241!1.12e-08!56;UBERON:0007135!1.12e-08!56;UBERON:0001893!1.94e-08!34;UBERON:0002346!2.03e-08!86;UBERON:0002780!5.00e-08!41;UBERON:0001890!5.00e-08!41;UBERON:0003080!5.00e-08!41;UBERON:0006240!5.00e-08!41;UBERON:0000073!5.31e-08!53;UBERON:0002616!5.31e-08!53;UBERON:0010371!3.24e-07!104;UBERON:0003528!5.50e-07!34;UBERON:0002020!5.50e-07!34
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}}
}}

Revision as of 15:03, 26 November 2012


Full id: C1719_melanoma_extraskeletal_Fibroblast_rhabdomyosarcoma_mesodermal_skeletal_normal



Phase1 CAGE Peaks

Hg19::chr14:32950745..32950751,-p@chr14:32950745..32950751
-
Hg19::chr14:32963433..32963487,+p4@AKAP6
Hg19::chr14:32963539..32963552,+p11@AKAP6
Hg19::chr14:32964466..32964503,+p7@AKAP6
Hg19::chr14:32964512..32964530,+p8@AKAP6


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>

Cell Type
Ontology termp-valuen
skin fibroblast2.07e-2323
fibroblast4.93e-0876
Uber Anatomy
Ontology termp-valuen
adult organism1.21e-15114
skin of body8.11e-1441
integument6.10e-1246
integumental system6.10e-1246
neural plate5.00e-0982
presumptive neural plate5.00e-0982
neural tube1.12e-0856
neural rod1.12e-0856
future spinal cord1.12e-0856
neural keel1.12e-0856
telencephalon1.94e-0834
neurectoderm2.03e-0886
regional part of forebrain5.00e-0841
forebrain5.00e-0841
anterior neural tube5.00e-0841
future forebrain5.00e-0841
regional part of nervous system5.31e-0853
regional part of brain5.31e-0853
ecto-epithelium3.24e-07104
brain grey matter5.50e-0734
gray matter5.50e-0734
Disease
Ontology termp-valuen
musculoskeletal system disease8.11e-185
myotonic disease8.11e-185
muscle tissue disease8.11e-185
myopathy8.11e-185
muscular disease8.11e-185
myotonic dystrophy8.11e-185


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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