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Coexpression cluster:C4605: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004121!1.21e-17!171;UBERON:0000924!1.21e-17!171;UBERON:0006601!1.21e-17!171;UBERON:0011216!1.58e-17!223;UBERON:0000064!1.29e-11!218;UBERON:0004119!2.94e-11!160;UBERON:0000925!2.94e-11!160;UBERON:0006595!2.94e-11!160;UBERON:0001004!8.88e-11!74;UBERON:0010371!1.48e-10!104;UBERON:0001016!1.54e-10!89;UBERON:0001017!1.86e-10!81;UBERON:0000481!4.40e-10!342;UBERON:0000062!1.06e-09!503;UBERON:0000477!1.72e-09!373;UBERON:0000955!5.29e-09!68;UBERON:0006238!5.29e-09!68;UBERON:0001007!6.54e-09!145;UBERON:0001555!6.54e-09!145;UBERON:0007026!6.54e-09!145;UBERON:0000161!8.80e-09!36;UBERON:0001049!4.70e-08!56;UBERON:0005068!4.70e-08!56;UBERON:0006241!4.70e-08!56;UBERON:0007135!4.70e-08!56;UBERON:0000073!5.21e-08!53;UBERON:0002616!5.21e-08!53;UBERON:0000480!6.01e-08!625;UBERON:0000922!6.25e-08!592;UBERON:0000166!7.19e-08!22;UBERON:0000467!7.28e-08!624;UBERON:0000468!3.08e-07!656;UBERON:0001893!3.80e-07!34;UBERON:0005423!4.47e-07!581;UBERON:0001869!4.62e-07!32;UBERON:0003102!4.63e-07!99;UBERON:0003528!7.17e-07!34;UBERON:0002020!7.17e-07!34;UBERON:0002791!7.77e-07!32;UBERON:0002346!8.59e-07!86;UBERON:0000065!8.92e-07!54;UBERON:0004921!9.69e-07!118
|ontology_enrichment_uberon=UBERON:0004121!1.21e-17!171;UBERON:0000924!1.21e-17!171;UBERON:0006601!1.21e-17!171;UBERON:0011216!1.58e-17!223;UBERON:0000064!1.29e-11!218;UBERON:0004119!2.94e-11!160;UBERON:0000925!2.94e-11!160;UBERON:0006595!2.94e-11!160;UBERON:0001004!8.88e-11!74;UBERON:0010371!1.48e-10!104;UBERON:0001016!1.54e-10!89;UBERON:0001017!1.86e-10!81;UBERON:0000481!4.40e-10!342;UBERON:0000062!1.06e-09!503;UBERON:0000477!1.72e-09!373;UBERON:0000955!5.29e-09!68;UBERON:0006238!5.29e-09!68;UBERON:0001007!6.54e-09!145;UBERON:0001555!6.54e-09!145;UBERON:0007026!6.54e-09!145;UBERON:0000161!8.80e-09!36;UBERON:0001049!4.70e-08!56;UBERON:0005068!4.70e-08!56;UBERON:0006241!4.70e-08!56;UBERON:0007135!4.70e-08!56;UBERON:0000073!5.21e-08!53;UBERON:0002616!5.21e-08!53;UBERON:0000480!6.01e-08!625;UBERON:0000922!6.25e-08!592;UBERON:0000166!7.19e-08!22;UBERON:0000467!7.28e-08!624;UBERON:0000468!3.08e-07!656;UBERON:0001893!3.80e-07!34;UBERON:0005423!4.47e-07!581;UBERON:0001869!4.62e-07!32;UBERON:0003102!4.63e-07!99;UBERON:0003528!7.17e-07!34;UBERON:0002020!7.17e-07!34;UBERON:0002791!7.77e-07!32;UBERON:0002346!8.59e-07!86;UBERON:0000065!8.92e-07!54;UBERON:0004921!9.69e-07!118
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}}
}}

Revision as of 16:50, 26 November 2012


Full id: C4605_keratoacanthoma_oral_Corneal_Mammary_epidermoid_Keratinocyte_Esophageal



Phase1 CAGE Peaks

Hg19::chr6:43423277..43423304,-p1@DLK2
Hg19::chr6:43423308..43423355,-p2@DLK2
Hg19::chr6:43423785..43423800,-p3@DLK2


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>

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.21e-17171
ectoderm1.21e-17171
presumptive ectoderm1.21e-17171
organ system subdivision1.58e-17223
organ part1.29e-11218
endoderm-derived structure2.94e-11160
endoderm2.94e-11160
presumptive endoderm2.94e-11160
respiratory system8.88e-1174
ecto-epithelium1.48e-10104
nervous system1.54e-1089
central nervous system1.86e-1081
multi-tissue structure4.40e-10342
organ1.06e-09503
anatomical cluster1.72e-09373
brain5.29e-0968
future brain5.29e-0968
digestive system6.54e-09145
digestive tract6.54e-09145
primitive gut6.54e-09145
orifice8.80e-0936
neural tube4.70e-0856
neural rod4.70e-0856
future spinal cord4.70e-0856
neural keel4.70e-0856
regional part of nervous system5.21e-0853
regional part of brain5.21e-0853
anatomical group6.01e-08625
embryo6.25e-08592
oral opening7.19e-0822
anatomical system7.28e-08624
multi-cellular organism3.08e-07656
telencephalon3.80e-0734
developing anatomical structure4.47e-07581
cerebral hemisphere4.62e-0732
surface structure4.63e-0799
brain grey matter7.17e-0734
gray matter7.17e-0734
regional part of telencephalon7.77e-0732
neurectoderm8.59e-0786
respiratory tract8.92e-0754
subdivision of digestive tract9.69e-07118
Disease
Ontology termp-valuen
cell type cancer4.40e-11143
carcinoma5.57e-11106
squamous cell carcinoma2.85e-1014


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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