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Coexpression cluster:C3867

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Full id: C3867_Prostate_esophagus_tongue_throat_amniotic_cervix_Gingival



Phase1 CAGE Peaks

Hg19::chr1:152487905..152487915,+p5@CRCT1
Hg19::chr1:152487916..152487926,+p2@CRCT1
Hg19::chr1:152975124..152975130,+p3@SPRR3


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


GO IDGO nameFDR corrected p-value
GO:0001533cornified envelope0.020706477803047
GO:0030216keratinocyte differentiation0.020706477803047
GO:0031424keratinization0.020706477803047
GO:0009913epidermal cell differentiation0.020706477803047
GO:0048730epidermis morphogenesis0.020706477803047
GO:0048729tissue morphogenesis0.0225832283381817
GO:0042060wound healing0.030495892973978
GO:0008544epidermis development0.030495892973978
GO:0007398ectoderm development0.030495892973978



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><br>


Uber Anatomy
Ontology termp-valuen
gingival epithelium1.66e-213
respiratory system5.00e-1672
respiratory tract1.00e-1353
endoderm-derived structure2.35e-12169
endoderm2.35e-12169
presumptive endoderm2.35e-12169
orifice1.06e-1135
oral opening1.57e-1121
segment of respiratory tract1.15e-1046
tongue1.78e-103
gustatory system1.78e-103
future tongue1.78e-103
trachea2.37e-097
respiratory airway2.37e-097
upper respiratory tract6.50e-0919
mouth1.63e-0828
stomodeum1.63e-0828
gingiva2.14e-088
tonsil2.69e-081
mucosa-associated lymphoid tissue2.69e-081
lymphoid tissue2.69e-081
tonsillar ring2.69e-081
digestive system3.33e-08155
digestive tract3.33e-08155
primitive gut3.33e-08155
tracheobronchial tree5.29e-0814
lower respiratory tract5.29e-0814
mixed endoderm/mesoderm-derived structure1.12e-07130
chordate pharynx6.85e-0710
pharyngeal region of foregut6.85e-0710


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
SUZ12#23512233.41052060737530.00117826764536030.0079979913306762



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.