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|ontology_enrichment_disease=DOID:1749!1.69e-23!14
|ontology_enrichment_disease=DOID:1749!1.69e-23!14
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}}
}}

Revision as of 19:01, 8 August 2012


Full id: C3242_Small_Tracheal_Bronchial_Mallassezderived_Keratinocyte_Gingival_Mammary



Phase1 CAGE Peaks

Hg19::chr12:116955659..116955671,+p1@ENST00000552992
Hg19::chr12:28187330..28187352,-p@chr12:28187330..28187352
-
Hg19::chr14:85799279..85799283,+p@chr14:85799279..85799283
+


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
general ecto-epithelial cell2.45e-2813
endo-epithelial cell2.33e-2743
respiratory epithelial cell1.82e-2313
epithelial cell7.61e-19254
endodermal cell2.16e-1859
squamous epithelial cell9.17e-1562
epidermal cell3.14e-148
stratified squamous epithelial cell1.21e-136
keratin accumulating cell1.21e-136
stratified epithelial cell1.21e-136
keratinizing barrier epithelial cell1.21e-136
epithelial fate stem cell1.21e-136
stratified epithelial stem cell1.21e-136
surface ectodermal cell1.21e-136
ecto-epithelial cell2.50e-1333
epithelial cell of tracheobronchial tree4.35e-139
epithelial cell of lower respiratory tract4.35e-139
bronchial epithelial cell4.79e-113
epithelial cell of Malassez8.58e-113
keratinocyte9.06e-115
duct epithelial cell1.01e-103
branched duct epithelial cell1.01e-103
tracheal epithelial cell1.01e-103
tracheoblast1.01e-103
gingival epithelial cell1.22e-103
epithelial cell of alimentary canal1.39e-1021
mammary gland epithelial cell1.30e-074
sebum secreting cell1.82e-072
epithelial cell of sweat gland1.82e-072
epithelial cell of skin gland1.82e-072
acinar cell of sebaceous gland1.82e-072
corneal epithelial cell2.34e-072
embryonic cell9.47e-07248
Uber Anatomy
Ontology termp-valuen
respiratory system1.81e-1572
surface structure8.47e-1495
orifice1.22e-1135
respiratory tract2.87e-1153
lower respiratory tract epithelium4.79e-113
epithelium of bronchus4.79e-113
gingival epithelium1.22e-103
skin epidermis2.26e-1014
outer epithelium2.26e-1014
enveloping layer of ectoderm2.26e-1014
oral opening2.33e-1021
mouth mucosa3.17e-105
endoderm-derived structure1.37e-09169
endoderm1.37e-09169
presumptive endoderm1.37e-09169
mouth3.49e-0928
stomodeum3.49e-0928
mucosa1.76e-0812
bronchus2.30e-084
jaw skeleton3.53e-084
tracheobronchial tree4.05e-0814
lower respiratory tract4.05e-0814
respiratory system epithelium1.07e-0728
mammary gland1.30e-074
mammary bud1.30e-074
mammary ridge1.30e-074
mammary placode1.30e-074
skin gland1.82e-072
epidermis gland1.82e-072
gland of integumental system1.82e-072
sebaceous gland1.82e-072
skin sebaceous gland1.82e-072
sweat gland1.82e-072
sweat gland placode1.82e-072
sebaceous gland placode1.82e-072
mucosa of oral region1.95e-074
respiratory system mucosa1.95e-074
neck2.06e-0710
segment of respiratory tract3.01e-0746
chordate pharynx3.06e-0710
pharyngeal region of foregut3.06e-0710
subdivision of head9.16e-0748
Disease
Ontology termp-valuen
squamous cell carcinoma1.69e-2314


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.