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Coexpression cluster:C2793: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!1.15e-37!114;UBERON:0001049!1.05e-13!56;UBERON:0005068!1.05e-13!56;UBERON:0006241!1.05e-13!56;UBERON:0007135!1.05e-13!56;UBERON:0000064!6.99e-12!218;UBERON:0000073!1.22e-11!53;UBERON:0002616!1.22e-11!53;UBERON:0003075!7.86e-11!82;UBERON:0007284!7.86e-11!82;UBERON:0001737!9.44e-11!9;UBERON:0001557!2.59e-10!19;UBERON:0010314!3.05e-10!132;UBERON:0011216!7.38e-10!223;UBERON:0002346!9.13e-10!86;UBERON:0002780!1.17e-09!41;UBERON:0001890!1.17e-09!41;UBERON:0003080!1.17e-09!41;UBERON:0006240!1.17e-09!41;UBERON:0001017!2.99e-09!81;UBERON:0000955!7.98e-09!68;UBERON:0006238!7.98e-09!68;UBERON:0003528!1.60e-08!34;UBERON:0002020!1.60e-08!34;UBERON:0001016!2.28e-08!89;UBERON:0001893!3.99e-08!34;UBERON:0000481!6.10e-08!342;UBERON:0003688!2.56e-07!6;UBERON:0002358!2.56e-07!6;UBERON:0003684!2.56e-07!6;UBERON:0001178!2.56e-07!6;UBERON:0002791!2.73e-07!32;UBERON:0001869!3.27e-07!32;UBERON:0000477!3.92e-07!373;UBERON:0004457!4.78e-07!12;UBERON:0000042!4.78e-07!12;UBERON:0000125!5.15e-07!9;UBERON:0002308!5.15e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.15e-37!114;UBERON:0001049!1.05e-13!56;UBERON:0005068!1.05e-13!56;UBERON:0006241!1.05e-13!56;UBERON:0007135!1.05e-13!56;UBERON:0000064!6.99e-12!218;UBERON:0000073!1.22e-11!53;UBERON:0002616!1.22e-11!53;UBERON:0003075!7.86e-11!82;UBERON:0007284!7.86e-11!82;UBERON:0001737!9.44e-11!9;UBERON:0001557!2.59e-10!19;UBERON:0010314!3.05e-10!132;UBERON:0011216!7.38e-10!223;UBERON:0002346!9.13e-10!86;UBERON:0002780!1.17e-09!41;UBERON:0001890!1.17e-09!41;UBERON:0003080!1.17e-09!41;UBERON:0006240!1.17e-09!41;UBERON:0001017!2.99e-09!81;UBERON:0000955!7.98e-09!68;UBERON:0006238!7.98e-09!68;UBERON:0003528!1.60e-08!34;UBERON:0002020!1.60e-08!34;UBERON:0001016!2.28e-08!89;UBERON:0001893!3.99e-08!34;UBERON:0000481!6.10e-08!342;UBERON:0003688!2.56e-07!6;UBERON:0002358!2.56e-07!6;UBERON:0003684!2.56e-07!6;UBERON:0001178!2.56e-07!6;UBERON:0002791!2.73e-07!32;UBERON:0001869!3.27e-07!32;UBERON:0000477!3.92e-07!373;UBERON:0004457!4.78e-07!12;UBERON:0000042!4.78e-07!12;UBERON:0000125!5.15e-07!9;UBERON:0002308!5.15e-07!9
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}}
}}

Revision as of 15:43, 26 November 2012


Full id: C2793_spleen_left_giant_lung_tongue_heart_mesothelioma



Phase1 CAGE Peaks

Hg19::chr4:41540215..41540226,+p15@LIMCH1
Hg19::chr4:41540251..41540269,+p11@LIMCH1
Hg19::chr4:41540295..41540302,+p16@LIMCH1
Hg19::chr4:41540314..41540341,+p6@LIMCH1


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>

Cell Type
Ontology termp-valuen
mesothelial cell2.58e-0719
Uber Anatomy
Ontology termp-valuen
adult organism1.15e-37114
neural tube1.05e-1356
neural rod1.05e-1356
future spinal cord1.05e-1356
neural keel1.05e-1356
organ part6.99e-12218
regional part of nervous system1.22e-1153
regional part of brain1.22e-1153
neural plate7.86e-1182
presumptive neural plate7.86e-1182
larynx9.44e-119
upper respiratory tract2.59e-1019
structure with developmental contribution from neural crest3.05e-10132
organ system subdivision7.38e-10223
neurectoderm9.13e-1086
regional part of forebrain1.17e-0941
forebrain1.17e-0941
anterior neural tube1.17e-0941
future forebrain1.17e-0941
central nervous system2.99e-0981
brain7.98e-0968
future brain7.98e-0968
brain grey matter1.60e-0834
gray matter1.60e-0834
nervous system2.28e-0889
telencephalon3.99e-0834
multi-tissue structure6.10e-08342
omentum2.56e-076
peritoneum2.56e-076
abdominal cavity2.56e-076
visceral peritoneum2.56e-076
regional part of telencephalon2.73e-0732
cerebral hemisphere3.27e-0732
anatomical cluster3.92e-07373
cavity lining4.78e-0712
serous membrane4.78e-0712
neural nucleus5.15e-079
nucleus of brain5.15e-079


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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