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Coexpression cluster:C1290: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!2.81e-50!114;UBERON:0001049!7.16e-17!56;UBERON:0005068!7.16e-17!56;UBERON:0006241!7.16e-17!56;UBERON:0007135!7.16e-17!56;UBERON:0000073!1.72e-14!53;UBERON:0002616!1.72e-14!53;UBERON:0001017!1.89e-13!81;UBERON:0003075!8.93e-13!82;UBERON:0007284!8.93e-13!82;UBERON:0000955!1.77e-12!68;UBERON:0006238!1.77e-12!68;UBERON:0002346!1.17e-11!86;UBERON:0010314!2.18e-11!132;UBERON:0011216!2.49e-11!223;UBERON:0002780!3.43e-11!41;UBERON:0001890!3.43e-11!41;UBERON:0003080!3.43e-11!41;UBERON:0006240!3.43e-11!41;UBERON:0001016!5.43e-11!89;UBERON:0000481!3.34e-09!342;UBERON:0000477!4.16e-09!373;UBERON:0003528!8.95e-09!34;UBERON:0002020!8.95e-09!34;UBERON:0001893!1.07e-08!34;UBERON:0010371!1.42e-08!104;UBERON:0002791!1.01e-07!32;UBERON:0001869!1.44e-07!32;UBERON:0000479!2.22e-07!773;UBERON:0003076!3.40e-07!15;UBERON:0003057!3.40e-07!15;UBERON:0002619!5.61e-07!22;UBERON:0001950!6.57e-07!20
|ontology_enrichment_uberon=UBERON:0007023!2.81e-50!114;UBERON:0001049!7.16e-17!56;UBERON:0005068!7.16e-17!56;UBERON:0006241!7.16e-17!56;UBERON:0007135!7.16e-17!56;UBERON:0000073!1.72e-14!53;UBERON:0002616!1.72e-14!53;UBERON:0001017!1.89e-13!81;UBERON:0003075!8.93e-13!82;UBERON:0007284!8.93e-13!82;UBERON:0000955!1.77e-12!68;UBERON:0006238!1.77e-12!68;UBERON:0002346!1.17e-11!86;UBERON:0010314!2.18e-11!132;UBERON:0011216!2.49e-11!223;UBERON:0002780!3.43e-11!41;UBERON:0001890!3.43e-11!41;UBERON:0003080!3.43e-11!41;UBERON:0006240!3.43e-11!41;UBERON:0001016!5.43e-11!89;UBERON:0000481!3.34e-09!342;UBERON:0000477!4.16e-09!373;UBERON:0003528!8.95e-09!34;UBERON:0002020!8.95e-09!34;UBERON:0001893!1.07e-08!34;UBERON:0010371!1.42e-08!104;UBERON:0002791!1.01e-07!32;UBERON:0001869!1.44e-07!32;UBERON:0000479!2.22e-07!773;UBERON:0003076!3.40e-07!15;UBERON:0003057!3.40e-07!15;UBERON:0002619!5.61e-07!22;UBERON:0001950!6.57e-07!20
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}}
}}

Revision as of 14:48, 26 November 2012


Full id: C1290_umbilical_skin_trachea_rectum_aorta_diaphragm_throat



Phase1 CAGE Peaks

Hg19::chr9:95165737..95165800,-p2@OGN
Hg19::chr9:95165802..95165820,-p4@OGN
Hg19::chr9:95165825..95165842,-p6@OGN
Hg19::chr9:95166842..95166867,-p1@OGN
Hg19::chr9:95166869..95166874,-p7@OGN
Hg19::chr9:95166884..95166908,-p3@OGN
Hg19::chr9:95166930..95166943,-p5@OGN


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.81e-50114
neural tube7.16e-1756
neural rod7.16e-1756
future spinal cord7.16e-1756
neural keel7.16e-1756
regional part of nervous system1.72e-1453
regional part of brain1.72e-1453
central nervous system1.89e-1381
neural plate8.93e-1382
presumptive neural plate8.93e-1382
brain1.77e-1268
future brain1.77e-1268
neurectoderm1.17e-1186
structure with developmental contribution from neural crest2.18e-11132
organ system subdivision2.49e-11223
regional part of forebrain3.43e-1141
forebrain3.43e-1141
anterior neural tube3.43e-1141
future forebrain3.43e-1141
nervous system5.43e-1189
multi-tissue structure3.34e-09342
anatomical cluster4.16e-09373
brain grey matter8.95e-0934
gray matter8.95e-0934
telencephalon1.07e-0834
ecto-epithelium1.42e-08104
regional part of telencephalon1.01e-0732
cerebral hemisphere1.44e-0732
tissue2.22e-07773
posterior neural tube3.40e-0715
chordal neural plate3.40e-0715
regional part of cerebral cortex5.61e-0722
neocortex6.57e-0720


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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