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Coexpression cluster:C3126: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!5.67e-18!114;UBERON:0004905!2.62e-13!8;UBERON:0000982!2.62e-13!8;UBERON:0004770!2.62e-13!8;UBERON:0011135!1.45e-11!5;UBERON:0002216!1.45e-11!5;UBERON:0011134!1.45e-11!5;UBERON:0002209!1.45e-11!5;UBERON:0002213!1.45e-11!5;UBERON:0005856!1.45e-11!5;UBERON:0005866!1.45e-11!5;UBERON:0005863!1.45e-11!5;UBERON:0007844!1.45e-11!5;UBERON:0011138!1.45e-11!5;UBERON:0001130!1.45e-11!5;UBERON:0001066!1.45e-11!5;UBERON:0001468!1.45e-11!5;UBERON:0007846!8.74e-08!3;UBERON:0000043!8.74e-08!3;UBERON:0007845!8.74e-08!3;UBERON:0002242!2.28e-07!3;UBERON:0003068!2.28e-07!3;UBERON:0002328!2.28e-07!3;UBERON:0004880!2.28e-07!3;UBERON:0003075!4.42e-07!82;UBERON:0007284!4.42e-07!82;UBERON:0002780!4.48e-07!41;UBERON:0001890!4.48e-07!41;UBERON:0003080!4.48e-07!41;UBERON:0006240!4.48e-07!41;UBERON:0000073!4.74e-07!53;UBERON:0002616!4.74e-07!53;UBERON:0003056!9.84e-07!61
|ontology_enrichment_uberon=UBERON:0007023!5.67e-18!114;UBERON:0004905!2.62e-13!8;UBERON:0000982!2.62e-13!8;UBERON:0004770!2.62e-13!8;UBERON:0011135!1.45e-11!5;UBERON:0002216!1.45e-11!5;UBERON:0011134!1.45e-11!5;UBERON:0002209!1.45e-11!5;UBERON:0002213!1.45e-11!5;UBERON:0005856!1.45e-11!5;UBERON:0005866!1.45e-11!5;UBERON:0005863!1.45e-11!5;UBERON:0007844!1.45e-11!5;UBERON:0011138!1.45e-11!5;UBERON:0001130!1.45e-11!5;UBERON:0001066!1.45e-11!5;UBERON:0001468!1.45e-11!5;UBERON:0007846!8.74e-08!3;UBERON:0000043!8.74e-08!3;UBERON:0007845!8.74e-08!3;UBERON:0002242!2.28e-07!3;UBERON:0003068!2.28e-07!3;UBERON:0002328!2.28e-07!3;UBERON:0004880!2.28e-07!3;UBERON:0003075!4.42e-07!82;UBERON:0007284!4.42e-07!82;UBERON:0002780!4.48e-07!41;UBERON:0001890!4.48e-07!41;UBERON:0003080!4.48e-07!41;UBERON:0006240!4.48e-07!41;UBERON:0000073!4.74e-07!53;UBERON:0002616!4.74e-07!53;UBERON:0003056!9.84e-07!61
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}}
}}

Revision as of 15:56, 26 November 2012


Full id: C3126_Anulus_Myoblast_tenocyte_Mesenchymal_Nucleus_immature_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr11:1892063..1892081,+p11@LSP1
Hg19::chr11:1892102..1892126,+p10@LSP1
Hg19::chr11:1892132..1892145,+p22@LSP1


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
adult organism5.67e-18114
articulation2.62e-138
skeletal joint2.62e-138
articular system2.62e-138
intervertebral cartilage1.45e-115
symphysis1.45e-115
nonsynovial joint1.45e-115
fibrous joint1.45e-115
cartilaginous joint1.45e-115
developing mesenchymal condensation1.45e-115
pre-cartilage condensation1.45e-115
cartilaginous condensation1.45e-115
cartilage element1.45e-115
post-cranial axial skeletal system1.45e-115
vertebral column1.45e-115
intervertebral disk1.45e-115
intervertebral joint1.45e-115
dense regular connective tissue8.74e-083
tendon8.74e-083
regular connective tissue8.74e-083
nucleus pulposus2.28e-073
axial mesoderm2.28e-073
notochord2.28e-073
chordamesoderm2.28e-073
neural plate4.42e-0782
presumptive neural plate4.42e-0782
regional part of forebrain4.48e-0741
forebrain4.48e-0741
anterior neural tube4.48e-0741
future forebrain4.48e-0741
regional part of nervous system4.74e-0753
regional part of brain4.74e-0753
pre-chordal neural plate9.84e-0761


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.