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Coexpression cluster:C4385

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Full id: C4385_Keratinocyte_Tracheal_Bronchial_Mallassezderived_Gingival_Sebocyte_oral



Phase1 CAGE Peaks

Hg19::chr4:15937715..15937733,-p@chr4:15937715..15937733
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Hg19::chr4:15939963..15939978,-p1@FGFBP1
Hg19::chr4:15939984..15939995,-p2@FGFBP1


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
endoderm-derived structure1.23e-25160
endoderm1.23e-25160
presumptive endoderm1.23e-25160
respiratory system3.57e-2274
digestive system1.24e-19145
digestive tract1.24e-19145
primitive gut1.24e-19145
respiratory tract9.62e-1854
subdivision of digestive tract7.04e-16118
respiratory primordium8.76e-1638
endoderm of foregut8.76e-1638
segment of respiratory tract6.43e-1547
foregut3.38e-1287
larynx6.66e-119
orifice7.04e-1136
mucosa4.68e-1020
endo-epithelium5.92e-1082
upper respiratory tract7.38e-0919
epithelial bud8.82e-0937
oral opening1.01e-0822
thoracic cavity element1.21e-0834
thoracic cavity1.21e-0834
organ segment1.47e-0898
thoracic segment organ3.09e-0835
anatomical space6.91e-0895
organ part7.54e-08218
female organism7.99e-0841
epithelial fold1.63e-0747
transitional epithelium1.78e-076
tracheobronchial tree2.21e-0715
lower respiratory tract2.21e-0715
epithelium of mucosa4.94e-078
head5.53e-0756
anterior region of body5.71e-0762
craniocervical region5.71e-0762
reproductive structure5.96e-0759
reproductive system5.96e-0759
urothelium6.17e-075
mouth8.55e-0729
stomodeum8.55e-0729
Disease
Ontology termp-valuen
carcinoma3.21e-26106
cell type cancer1.68e-16143
squamous cell carcinoma2.67e-1414
adenocarcinoma4.30e-1025
cancer1.46e-09235
disease of cellular proliferation2.15e-09239


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
PRDM1#639287.88730385164050.0001716248848029080.00209225298750215



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.