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Coexpression cluster:C1194: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000475!1.53e-11!264;UBERON:0000481!5.66e-11!342;UBERON:0003103!6.39e-11!68;UBERON:0003104!2.93e-10!160;UBERON:0009142!2.93e-10!160;UBERON:0002385!9.01e-09!64;UBERON:0001015!9.01e-09!64;UBERON:0000383!9.01e-09!64;UBERON:0001048!1.26e-08!160;UBERON:0007503!2.02e-08!78;UBERON:0003135!2.99e-08!11;UBERON:0007524!3.17e-08!73;UBERON:0002329!3.96e-08!71;UBERON:0003059!3.96e-08!71;UBERON:0007282!3.96e-08!71;UBERON:0004290!3.96e-08!71;UBERON:0009618!3.96e-08!71;UBERON:0001134!4.71e-08!62;UBERON:0002036!4.71e-08!62;UBERON:0003082!4.71e-08!62;UBERON:0003077!7.04e-08!72;UBERON:0007285!7.04e-08!72;UBERON:0003886!1.03e-07!54;UBERON:0000468!1.28e-07!656;UBERON:0005631!1.50e-07!14;UBERON:0000158!1.50e-07!14;UBERON:0000464!1.62e-07!95;UBERON:0000991!1.78e-07!21;UBERON:0009196!1.78e-07!21;UBERON:0009117!1.78e-07!21;UBERON:0005564!1.78e-07!21;UBERON:0007100!2.80e-07!27;UBERON:0002100!3.26e-07!199;UBERON:0002553!3.80e-07!61;UBERON:0004176!6.06e-07!22;UBERON:0002323!6.38e-07!46;UBERON:0007625!7.27e-07!11
|ontology_enrichment_uberon=UBERON:0000475!1.53e-11!264;UBERON:0000481!5.66e-11!342;UBERON:0003103!6.39e-11!68;UBERON:0003104!2.93e-10!160;UBERON:0009142!2.93e-10!160;UBERON:0002385!9.01e-09!64;UBERON:0001015!9.01e-09!64;UBERON:0000383!9.01e-09!64;UBERON:0001048!1.26e-08!160;UBERON:0007503!2.02e-08!78;UBERON:0003135!2.99e-08!11;UBERON:0007524!3.17e-08!73;UBERON:0002329!3.96e-08!71;UBERON:0003059!3.96e-08!71;UBERON:0007282!3.96e-08!71;UBERON:0004290!3.96e-08!71;UBERON:0009618!3.96e-08!71;UBERON:0001134!4.71e-08!62;UBERON:0002036!4.71e-08!62;UBERON:0003082!4.71e-08!62;UBERON:0003077!7.04e-08!72;UBERON:0007285!7.04e-08!72;UBERON:0003886!1.03e-07!54;UBERON:0000468!1.28e-07!656;UBERON:0005631!1.50e-07!14;UBERON:0000158!1.50e-07!14;UBERON:0000464!1.62e-07!95;UBERON:0000991!1.78e-07!21;UBERON:0009196!1.78e-07!21;UBERON:0009117!1.78e-07!21;UBERON:0005564!1.78e-07!21;UBERON:0007100!2.80e-07!27;UBERON:0002100!3.26e-07!199;UBERON:0002553!3.80e-07!61;UBERON:0004176!6.06e-07!22;UBERON:0002323!6.38e-07!46;UBERON:0007625!7.27e-07!11
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}}
}}

Revision as of 14:44, 26 November 2012


Full id: C1194_skeletal_large_diaphragm_throat_trachea_testicular_tongue



Phase1 CAGE Peaks

Hg19::chr14:101398219..101398220,+p@chr14:101398219..101398220
+
Hg19::chrX:105066342..105066377,+p5@NRK
Hg19::chrX:105066381..105066395,+p6@NRK
Hg19::chrX:105066499..105066514,+p2@NRK
Hg19::chrX:105066524..105066552,+p1@NRK
Hg19::chrX:105066554..105066569,+p3@NRK
Hg19::chrX:105066764..105066790,+p4@NRK


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><br>

Cell Type
Ontology termp-valuen
contractile cell3.01e-0959
cell of skeletal muscle4.91e-089
muscle cell1.16e-0755
muscle precursor cell7.50e-0758
myoblast7.50e-0758
multi-potent skeletal muscle stem cell7.50e-0758
electrically responsive cell8.69e-0761
electrically active cell8.69e-0761
Uber Anatomy
Ontology termp-valuen
organism subdivision1.53e-11264
multi-tissue structure5.66e-11342
compound organ6.39e-1168
mesenchyme2.93e-10160
entire embryonic mesenchyme2.93e-10160
muscle tissue9.01e-0964
musculature9.01e-0964
musculature of body9.01e-0964
primordium1.26e-08160
epithelial vesicle2.02e-0878
male reproductive organ2.99e-0811
dense mesenchyme tissue3.17e-0873
somite3.96e-0871
presomitic mesoderm3.96e-0871
presumptive segmental plate3.96e-0871
dermomyotome3.96e-0871
trunk paraxial mesoderm3.96e-0871
skeletal muscle tissue4.71e-0862
striated muscle tissue4.71e-0862
myotome4.71e-0862
paraxial mesoderm7.04e-0872
presumptive paraxial mesoderm7.04e-0872
body cavity precursor1.03e-0754
multi-cellular organism1.28e-07656
extraembryonic membrane1.50e-0714
membranous layer1.50e-0714
anatomical space1.62e-0795
gonad1.78e-0721
indifferent external genitalia1.78e-0721
indifferent gonad1.78e-0721
gonad primordium1.78e-0721
primary circulatory organ2.80e-0727
trunk3.26e-07199
anatomical cavity3.80e-0761
external genitalia6.06e-0722
body cavity6.38e-0746
pigment epithelium of eye7.27e-0711


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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