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Coexpression cluster:C3872

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Full id: C3872_tongue_Prostate_Bronchial_Sebocyte_Keratinocyte_Corneal_Urothelial



Phase1 CAGE Peaks

Hg19::chr1:153587142..153587155,-p@chr1:153587142..153587155
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Hg19::chr1:153587170..153587185,-p@chr1:153587170..153587185
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Hg19::chr1:153587360..153587377,-p@chr1:153587360..153587377
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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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.18e-14160
endoderm3.18e-14160
presumptive endoderm3.18e-14160
orifice5.43e-1236
surface structure2.11e-1199
oral opening9.25e-1122
mammary gland1.03e-104
mammary bud1.03e-104
mammary ridge1.03e-104
mammary placode1.03e-104
digestive system3.61e-10145
digestive tract3.61e-10145
primitive gut3.61e-10145
lower respiratory tract epithelium4.86e-103
epithelium of bronchus4.86e-103
mouth mucosa8.48e-1013
mucosa1.35e-0920
tongue2.06e-093
gustatory system2.06e-093
future tongue2.06e-093
mouth2.22e-0929
stomodeum2.22e-0929
gingival epithelium2.25e-093
respiratory system3.38e-0974
anterior region of body6.95e-0962
craniocervical region6.95e-0962
epithelial fold1.52e-0847
epithelial bud2.82e-0837
head1.03e-0756
skin gland4.02e-072
epidermis gland4.02e-072
gland of integumental system4.02e-072
sebaceous gland4.02e-072
skin sebaceous gland4.02e-072
sweat gland4.02e-072
sweat gland placode4.02e-072
sebaceous gland placode4.02e-072
subdivision of head7.76e-0749
mucosa of oral region8.23e-074
respiratory system mucosa8.23e-074
neck8.59e-0710
Disease
Ontology termp-valuen
squamous cell carcinoma9.65e-0914
thoracic cancer8.74e-074
breast cancer8.74e-074


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
CTCF#1066435.360256373075030.0064925092527670.0279513242033774



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.