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Coexpression cluster:C4384

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Full id: C4384_squamous_oral_serous_Corneal_Gingival_bronchioalveolar_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr4:15920199..15920212,+p@chr4:15920199..15920212
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Hg19::chr4:15920326..15920338,+p@chr4:15920326..15920338
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Hg19::chr4:15920342..15920362,+p@chr4:15920342..15920362
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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
endo-epithelial cell5.02e-5142
endodermal cell8.26e-3858
epithelial cell3.65e-31253
respiratory epithelial cell5.30e-2913
epithelial cell of alimentary canal1.79e-2120
epithelial cell of tracheobronchial tree6.81e-189
epithelial cell of lower respiratory tract6.81e-189
gingival epithelial cell1.29e-113
duct epithelial cell4.27e-113
branched duct epithelial cell4.27e-113
tracheal epithelial cell4.27e-113
tracheoblast4.27e-113
bronchial epithelial cell1.06e-103
squamous epithelial cell4.43e-1063
embryonic cell6.13e-10250
stratified squamous epithelial cell1.32e-096
keratin accumulating cell1.32e-096
stratified epithelial cell1.32e-096
keratinizing barrier epithelial cell1.32e-096
epithelial fate stem cell1.32e-096
stratified epithelial stem cell1.32e-096
surface ectodermal cell1.32e-096
general ecto-epithelial cell1.02e-0814
corneal epithelial cell2.30e-082
keratinocyte4.36e-075
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.80e-15160
endoderm6.80e-15160
presumptive endoderm6.80e-15160
respiratory system1.44e-1474
tracheobronchial tree4.03e-1315
lower respiratory tract4.03e-1315
mouth mucosa3.07e-1213
gingival epithelium1.29e-113
lower respiratory tract epithelium1.06e-103
epithelium of bronchus1.06e-103
digestive system1.83e-10145
digestive tract1.83e-10145
primitive gut1.83e-10145
mucosa6.52e-1020
orifice5.82e-0936
respiratory tract9.18e-0954
oral opening1.05e-0822
mucosa of oral region2.49e-084
respiratory system mucosa2.49e-084
thoracic cavity element6.39e-0834
thoracic cavity6.39e-0834
mouth7.09e-0829
stomodeum7.09e-0829
trachea8.51e-087
respiratory airway8.51e-087
thoracic segment organ1.22e-0735
epithelial fold1.32e-0747
endo-epithelium1.65e-0782
epithelial bud6.60e-0737
surface structure8.97e-0799
Disease
Ontology termp-valuen
squamous cell carcinoma3.11e-1814
carcinoma2.01e-09106


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.