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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4384_squamous_oral_serous_Corneal_Gingival_bronchioalveolar_Keratinocyte
|full_id=C4384_squamous_oral_serous_Corneal_Gingival_bronchioalveolar_Keratinocyte
|id=C4384
|id=C4384

Revision as of 17:27, 12 September 2012


Full id: C4384_squamous_oral_serous_Corneal_Gingival_bronchioalveolar_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr4:15920199..15920212,+p@chr4:15920199..15920212
+
Hg19::chr4:15920326..15920338,+p@chr4:15920326..15920338
+
Hg19::chr4:15920342..15920362,+p@chr4:15920342..15920362
+


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
respiratory system6.06e-1572
endoderm-derived structure2.42e-14169
endoderm2.42e-14169
presumptive endoderm2.42e-14169
respiratory tract3.66e-1053
digestive system7.71e-10155
digestive tract7.71e-10155
primitive gut7.71e-10155
tracheobronchial tree8.22e-0914
lower respiratory tract8.22e-0914
anatomical space1.18e-08104
oral opening2.48e-0821
gingival epithelium6.17e-083
immaterial anatomical entity7.19e-08126
endo-epithelium8.59e-0882
thoracic cavity element2.05e-0734
thoracic cavity2.05e-0734
epithelial fold2.15e-0751
segment of respiratory tract2.46e-0746
mouth mucosa2.49e-075
duct2.66e-0726
orifice2.97e-0735
lower respiratory tract epithelium3.02e-073
epithelium of bronchus3.02e-073
thoracic segment organ4.07e-0735
subdivision of digestive tract4.50e-07129
endodermal part of digestive tract4.50e-07129
renal cortex tubule5.17e-073
region of nephron tubule5.17e-073
proximal tubule5.17e-073
cortex5.29e-0716
mouth5.77e-0728
stomodeum5.77e-0728
foregut6.29e-0798
respiratory system epithelium7.36e-0728
Disease
Ontology termp-valuen
squamous cell carcinoma8.56e-1414
carcinoma1.03e-11106
cell type cancer5.49e-09143


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
GATA2#2624312.7449317335540.0004829527704283790.00438219847009292



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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