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Coexpression cluster:C2852: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000481!2.61e-15!342;UBERON:0000475!1.59e-11!264;UBERON:0007023!1.88e-11!114;UBERON:0004119!1.71e-10!160;UBERON:0000925!1.71e-10!160;UBERON:0006595!1.71e-10!160;UBERON:0001048!3.34e-10!160;UBERON:0000477!3.39e-10!373;UBERON:0004111!3.40e-10!240;UBERON:0004921!1.73e-09!118;UBERON:0000922!3.55e-09!592;UBERON:0005256!4.46e-09!122;UBERON:0002100!4.61e-09!199;UBERON:0000466!6.57e-09!117;UBERON:0003914!7.09e-09!117;UBERON:0001007!1.05e-08!145;UBERON:0001555!1.05e-08!145;UBERON:0007026!1.05e-08!145;UBERON:0001041!1.77e-08!87;UBERON:0003104!1.98e-08!160;UBERON:0009142!1.98e-08!160;UBERON:0005423!2.18e-08!581;UBERON:0000923!4.49e-08!560;UBERON:0010316!4.49e-08!560;UBERON:0005291!4.49e-08!560;UBERON:0006598!4.49e-08!560;UBERON:0010317!4.49e-08!560;UBERON:0002532!4.49e-08!560;UBERON:0000468!5.30e-08!656;UBERON:0002050!7.13e-08!564;UBERON:0000025!8.98e-08!192;UBERON:0000483!9.13e-08!306;UBERON:0000119!2.15e-07!309;UBERON:0009497!4.04e-07!25;UBERON:0000015!4.04e-07!25;UBERON:0002423!4.04e-07!25;UBERON:0006235!4.04e-07!25;UBERON:0004161!4.04e-07!25;UBERON:0001044!9.71e-07!6;UBERON:0003293!9.71e-07!6;UBERON:0003294!9.71e-07!6;UBERON:0010047!9.71e-07!6;UBERON:0000167!9.71e-07!6
|ontology_enrichment_uberon=UBERON:0000481!2.61e-15!342;UBERON:0000475!1.59e-11!264;UBERON:0007023!1.88e-11!114;UBERON:0004119!1.71e-10!160;UBERON:0000925!1.71e-10!160;UBERON:0006595!1.71e-10!160;UBERON:0001048!3.34e-10!160;UBERON:0000477!3.39e-10!373;UBERON:0004111!3.40e-10!240;UBERON:0004921!1.73e-09!118;UBERON:0000922!3.55e-09!592;UBERON:0005256!4.46e-09!122;UBERON:0002100!4.61e-09!199;UBERON:0000466!6.57e-09!117;UBERON:0003914!7.09e-09!117;UBERON:0001007!1.05e-08!145;UBERON:0001555!1.05e-08!145;UBERON:0007026!1.05e-08!145;UBERON:0001041!1.77e-08!87;UBERON:0003104!1.98e-08!160;UBERON:0009142!1.98e-08!160;UBERON:0005423!2.18e-08!581;UBERON:0000923!4.49e-08!560;UBERON:0010316!4.49e-08!560;UBERON:0005291!4.49e-08!560;UBERON:0006598!4.49e-08!560;UBERON:0010317!4.49e-08!560;UBERON:0002532!4.49e-08!560;UBERON:0000468!5.30e-08!656;UBERON:0002050!7.13e-08!564;UBERON:0000025!8.98e-08!192;UBERON:0000483!9.13e-08!306;UBERON:0000119!2.15e-07!309;UBERON:0009497!4.04e-07!25;UBERON:0000015!4.04e-07!25;UBERON:0002423!4.04e-07!25;UBERON:0006235!4.04e-07!25;UBERON:0004161!4.04e-07!25;UBERON:0001044!9.71e-07!6;UBERON:0003293!9.71e-07!6;UBERON:0003294!9.71e-07!6;UBERON:0010047!9.71e-07!6;UBERON:0000167!9.71e-07!6
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}}
}}

Revision as of 15:45, 26 November 2012


Full id: C2852_mesenchymal_Mesothelial_skeletal_diaphragm_aorta_Hepatocyte_salivary



Phase1 CAGE Peaks

Hg19::chr6:160769373..160769384,+p2@SLC22A3
Hg19::chr6:160769399..160769416,+p1@SLC22A3
Hg19::chr6:160769591..160769601,+p3@SLC22A3
Hg19::chr6:160831761..160831769,+p@chr6:160831761..160831769
+


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure2.61e-15342
organism subdivision1.59e-11264
adult organism1.88e-11114
endoderm-derived structure1.71e-10160
endoderm1.71e-10160
presumptive endoderm1.71e-10160
primordium3.34e-10160
anatomical cluster3.39e-10373
anatomical conduit3.40e-10240
subdivision of digestive tract1.73e-09118
embryo3.55e-09592
trunk mesenchyme4.46e-09122
trunk4.61e-09199
immaterial anatomical entity6.57e-09117
epithelial tube7.09e-09117
digestive system1.05e-08145
digestive tract1.05e-08145
primitive gut1.05e-08145
foregut1.77e-0887
mesenchyme1.98e-08160
entire embryonic mesenchyme1.98e-08160
developing anatomical structure2.18e-08581
germ layer4.49e-08560
germ layer / neural crest4.49e-08560
embryonic tissue4.49e-08560
presumptive structure4.49e-08560
germ layer / neural crest derived structure4.49e-08560
epiblast (generic)4.49e-08560
multi-cellular organism5.30e-08656
embryonic structure7.13e-08564
tube8.98e-08192
epithelium9.13e-08306
cell layer2.15e-07309
epithelium of foregut-midgut junction4.04e-0725
anatomical boundary4.04e-0725
hepatobiliary system4.04e-0725
foregut-midgut junction4.04e-0725
septum transversum4.04e-0725
saliva-secreting gland9.71e-076
gland of oral region9.71e-076
gland of foregut9.71e-076
oral gland9.71e-076
oral cavity9.71e-076
Disease
Ontology termp-valuen
ovarian cancer1.47e-0814


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.

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