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Coexpression cluster:C2792: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!9.09e-31!114;UBERON:0001049!4.89e-13!56;UBERON:0005068!4.89e-13!56;UBERON:0006241!4.89e-13!56;UBERON:0007135!4.89e-13!56;UBERON:0000064!3.58e-12!218;UBERON:0000073!3.41e-11!53;UBERON:0002616!3.41e-11!53;UBERON:0001737!2.41e-10!9;UBERON:0001017!2.37e-09!81;UBERON:0000955!3.49e-09!68;UBERON:0006238!3.49e-09!68;UBERON:0011216!6.24e-09!223;UBERON:0001557!2.29e-08!19;UBERON:0002780!2.41e-08!41;UBERON:0001890!2.41e-08!41;UBERON:0003080!2.41e-08!41;UBERON:0006240!2.41e-08!41;UBERON:0010314!3.70e-08!132;UBERON:0003528!4.00e-08!34;UBERON:0002020!4.00e-08!34;UBERON:0003075!4.03e-08!82;UBERON:0007284!4.03e-08!82;UBERON:0004457!6.46e-08!12;UBERON:0000042!6.46e-08!12;UBERON:0001893!9.36e-08!34;UBERON:0000062!1.52e-07!503;UBERON:0001016!2.88e-07!89;UBERON:0003688!2.92e-07!6;UBERON:0002358!2.92e-07!6;UBERON:0003684!2.92e-07!6;UBERON:0001178!2.92e-07!6;UBERON:0002346!3.13e-07!86;UBERON:0000481!3.27e-07!342;UBERON:0002791!6.51e-07!32;UBERON:0001869!7.98e-07!32
|ontology_enrichment_uberon=UBERON:0007023!9.09e-31!114;UBERON:0001049!4.89e-13!56;UBERON:0005068!4.89e-13!56;UBERON:0006241!4.89e-13!56;UBERON:0007135!4.89e-13!56;UBERON:0000064!3.58e-12!218;UBERON:0000073!3.41e-11!53;UBERON:0002616!3.41e-11!53;UBERON:0001737!2.41e-10!9;UBERON:0001017!2.37e-09!81;UBERON:0000955!3.49e-09!68;UBERON:0006238!3.49e-09!68;UBERON:0011216!6.24e-09!223;UBERON:0001557!2.29e-08!19;UBERON:0002780!2.41e-08!41;UBERON:0001890!2.41e-08!41;UBERON:0003080!2.41e-08!41;UBERON:0006240!2.41e-08!41;UBERON:0010314!3.70e-08!132;UBERON:0003528!4.00e-08!34;UBERON:0002020!4.00e-08!34;UBERON:0003075!4.03e-08!82;UBERON:0007284!4.03e-08!82;UBERON:0004457!6.46e-08!12;UBERON:0000042!6.46e-08!12;UBERON:0001893!9.36e-08!34;UBERON:0000062!1.52e-07!503;UBERON:0001016!2.88e-07!89;UBERON:0003688!2.92e-07!6;UBERON:0002358!2.92e-07!6;UBERON:0003684!2.92e-07!6;UBERON:0001178!2.92e-07!6;UBERON:0002346!3.13e-07!86;UBERON:0000481!3.27e-07!342;UBERON:0002791!6.51e-07!32;UBERON:0001869!7.98e-07!32
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}}
}}

Revision as of 15:43, 26 November 2012


Full id: C2792_lung_Preadipocyte_Adipocyte_mesothelioma_spleen_mucinous_skeletal



Phase1 CAGE Peaks

Hg19::chr4:41540152..41540157,+p20@LIMCH1
Hg19::chr4:41540160..41540196,+p3@LIMCH1
Hg19::chr4:41540197..41540212,+p10@LIMCH1
Hg19::chr4:41540273..41540283,+p17@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 cell2.63e-0919
Uber Anatomy
Ontology termp-valuen
adult organism9.09e-31114
neural tube4.89e-1356
neural rod4.89e-1356
future spinal cord4.89e-1356
neural keel4.89e-1356
organ part3.58e-12218
regional part of nervous system3.41e-1153
regional part of brain3.41e-1153
larynx2.41e-109
central nervous system2.37e-0981
brain3.49e-0968
future brain3.49e-0968
organ system subdivision6.24e-09223
upper respiratory tract2.29e-0819
regional part of forebrain2.41e-0841
forebrain2.41e-0841
anterior neural tube2.41e-0841
future forebrain2.41e-0841
structure with developmental contribution from neural crest3.70e-08132
brain grey matter4.00e-0834
gray matter4.00e-0834
neural plate4.03e-0882
presumptive neural plate4.03e-0882
cavity lining6.46e-0812
serous membrane6.46e-0812
telencephalon9.36e-0834
organ1.52e-07503
nervous system2.88e-0789
omentum2.92e-076
peritoneum2.92e-076
abdominal cavity2.92e-076
visceral peritoneum2.92e-076
neurectoderm3.13e-0786
multi-tissue structure3.27e-07342
regional part of telencephalon6.51e-0732
cerebral hemisphere7.98e-0732


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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