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Coexpression cluster:C2335: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004119!5.56e-16!160;UBERON:0000925!5.56e-16!160;UBERON:0006595!5.56e-16!160;UBERON:0007023!2.85e-12!114;UBERON:0001004!3.12e-12!74;UBERON:0000161!8.83e-12!36;UBERON:0000166!2.71e-10!22;UBERON:0001007!2.75e-09!145;UBERON:0001555!2.75e-09!145;UBERON:0007026!2.75e-09!145;UBERON:0005631!2.82e-09!14;UBERON:0000158!2.82e-09!14;UBERON:0000165!4.79e-09!29;UBERON:0000930!4.79e-09!29;UBERON:0003102!5.61e-09!99;UBERON:0005910!2.69e-08!6;UBERON:0000065!6.40e-08!54;UBERON:0001044!7.75e-08!6;UBERON:0003293!7.75e-08!6;UBERON:0003294!7.75e-08!6;UBERON:0010047!7.75e-08!6;UBERON:0000167!7.75e-08!6;UBERON:0005178!1.02e-07!34;UBERON:0002224!1.02e-07!34;UBERON:0000365!1.03e-07!5;UBERON:0000464!1.22e-07!95;UBERON:0000153!2.15e-07!62;UBERON:0007811!2.15e-07!62;UBERON:0005181!2.33e-07!35;UBERON:0000062!4.50e-07!503
|ontology_enrichment_uberon=UBERON:0004119!5.56e-16!160;UBERON:0000925!5.56e-16!160;UBERON:0006595!5.56e-16!160;UBERON:0007023!2.85e-12!114;UBERON:0001004!3.12e-12!74;UBERON:0000161!8.83e-12!36;UBERON:0000166!2.71e-10!22;UBERON:0001007!2.75e-09!145;UBERON:0001555!2.75e-09!145;UBERON:0007026!2.75e-09!145;UBERON:0005631!2.82e-09!14;UBERON:0000158!2.82e-09!14;UBERON:0000165!4.79e-09!29;UBERON:0000930!4.79e-09!29;UBERON:0003102!5.61e-09!99;UBERON:0005910!2.69e-08!6;UBERON:0000065!6.40e-08!54;UBERON:0001044!7.75e-08!6;UBERON:0003293!7.75e-08!6;UBERON:0003294!7.75e-08!6;UBERON:0010047!7.75e-08!6;UBERON:0000167!7.75e-08!6;UBERON:0005178!1.02e-07!34;UBERON:0002224!1.02e-07!34;UBERON:0000365!1.03e-07!5;UBERON:0000464!1.22e-07!95;UBERON:0000153!2.15e-07!62;UBERON:0007811!2.15e-07!62;UBERON:0005181!2.33e-07!35;UBERON:0000062!4.50e-07!503
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}}
}}

Revision as of 15:26, 26 November 2012


Full id: C2335_lung_immature_thyroid_salivary_esophagus_ductus_tongue



Phase1 CAGE Peaks

Hg19::chr15:45422041..45422052,-p2@DUOXA1
Hg19::chr15:45422056..45422086,-p1@DUOXA1
Hg19::chr15:45422163..45422172,+p2@DUOX1
Hg19::chr15:45422178..45422201,+p1@DUOX1


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:0050665hydrogen peroxide biosynthetic process0.0038853240511488
GO:0042335cuticle development0.0038853240511488
GO:0016174NAD(P)H oxidase activity0.0038853240511488
GO:0042554superoxide release0.0038853240511488
GO:0050664oxidoreductase activity, acting on NADH or NADPH, with oxygen as acceptor0.0038853240511488
GO:0051591response to cAMP0.00631290812271665
GO:0042744hydrogen peroxide catabolic process0.00631290812271665
GO:0042743hydrogen peroxide metabolic process0.00631290812271665
GO:0042542response to hydrogen peroxide0.00815725894822441
GO:0006801superoxide metabolic process0.00815725894822441
GO:0000302response to reactive oxygen species0.00953361626905974
GO:0050661NADP binding0.0116491094420604
GO:0042446hormone biosynthetic process0.0116491094420604
GO:0019221cytokine and chemokine mediated signaling pathway0.0116491094420604
GO:0006800oxygen and reactive oxygen species metabolic process0.0116491094420604
GO:0010033response to organic substance0.0138924756148232
GO:0004601peroxidase activity0.0138924756148232
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0138924756148232
GO:0016324apical plasma membrane0.0138924756148232
GO:0045177apical part of cell0.016261466958797
GO:0042445hormone metabolic process0.016261466958797
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.0190444920081179
GO:0050660FAD binding0.0192267960029108
GO:0006979response to oxidative stress0.019393736430353
GO:0050662coenzyme binding0.0416988764963919
GO:0020037heme binding0.0416988764963919
GO:0046906tetrapyrrole binding0.0416988764963919



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
endoderm-derived structure5.56e-16160
endoderm5.56e-16160
presumptive endoderm5.56e-16160
adult organism2.85e-12114
respiratory system3.12e-1274
orifice8.83e-1236
oral opening2.71e-1022
digestive system2.75e-09145
digestive tract2.75e-09145
primitive gut2.75e-09145
extraembryonic membrane2.82e-0914
membranous layer2.82e-0914
mouth4.79e-0929
stomodeum4.79e-0929
surface structure5.61e-0999
transitional epithelium2.69e-086
respiratory tract6.40e-0854
saliva-secreting gland7.75e-086
gland of oral region7.75e-086
gland of foregut7.75e-086
oral gland7.75e-086
oral cavity7.75e-086
thoracic cavity element1.02e-0734
thoracic cavity1.02e-0734
urothelium1.03e-075
anatomical space1.22e-0795
anterior region of body2.15e-0762
craniocervical region2.15e-0762
thoracic segment organ2.33e-0735
organ4.50e-07503


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)

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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


No analysis results for this cluster

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.