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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4605_keratoacanthoma_oral_Corneal_Mammary_epidermoid_Keratinocyte_Esophageal
|full_id=C4605_keratoacanthoma_oral_Corneal_Mammary_epidermoid_Keratinocyte_Esophageal
|id=C4605
|id=C4605

Revision as of 17:42, 12 September 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>


Cell Type
Ontology termp-valuen
epithelial cell5.59e-13254
endo-epithelial cell1.18e-1143
endodermal cell1.99e-1059
general ecto-epithelial cell2.40e-0713
Uber Anatomy
Ontology termp-valuen
ectoderm9.14e-21173
presumptive ectoderm9.14e-21173
ectoderm-derived structure1.36e-20169
anterior region of body2.12e-18129
craniocervical region2.12e-18129
head2.18e-17123
endoderm-derived structure1.59e-15169
endoderm1.59e-15169
presumptive endoderm1.59e-15169
multi-tissue structure5.65e-15347
organ part2.44e-14219
organism subdivision2.66e-14365
organ2.44e-13511
digestive system1.82e-12155
digestive tract1.82e-12155
primitive gut1.82e-12155
respiratory system2.26e-1272
central nervous system2.66e-1282
regional part of nervous system4.60e-1294
nervous system4.60e-1294
neurectoderm4.48e-1190
neural tube4.56e-1157
neural rod4.56e-1157
future spinal cord4.56e-1157
neural keel4.56e-1157
neural plate5.59e-1186
presumptive neural plate5.59e-1186
brain6.76e-1169
future brain6.76e-1169
embryo2.63e-10612
subdivision of digestive tract6.05e-10129
endodermal part of digestive tract6.05e-10129
cerebral hemisphere9.05e-1032
embryonic structure1.00e-09605
developing anatomical structure1.00e-09605
telencephalon1.21e-0934
anterior neural tube1.34e-0942
germ layer1.49e-09604
embryonic tissue1.49e-09604
presumptive structure1.49e-09604
epiblast (generic)1.49e-09604
pre-chordal neural plate2.37e-0961
anatomical group2.41e-09626
anatomical system2.57e-09625
regional part of telencephalon2.82e-0933
regional part of forebrain3.24e-0941
forebrain3.24e-0941
future forebrain3.24e-0941
gray matter3.56e-0934
brain grey matter3.56e-0934
multi-cellular organism5.27e-09659
respiratory tract5.49e-0953
mixed endoderm/mesoderm-derived structure6.79e-09130
regional part of brain7.33e-0959
foregut2.56e-0898
segment of respiratory tract5.11e-0846
cerebral cortex6.94e-0825
pallium6.94e-0825
regional part of cerebral cortex1.73e-0722
neocortex1.75e-0720
oral opening5.32e-0721
orifice8.15e-0735
epithelium8.22e-07309
Disease
Ontology termp-valuen
carcinoma6.95e-11106
cell type cancer1.15e-10143
squamous cell carcinoma1.83e-0914


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.