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Coexpression cluster:C2469: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007100!3.84e-35!27;UBERON:0000948!3.30e-24!24;UBERON:0005498!3.30e-24!24;UBERON:0004140!3.30e-24!24;UBERON:0009881!3.30e-24!24;UBERON:0004141!3.30e-24!24;UBERON:0003084!3.30e-24!24;UBERON:0007005!3.30e-24!24;UBERON:0004139!3.30e-24!24;UBERON:0004291!3.30e-24!24;UBERON:0007023!2.63e-20!114;UBERON:0003103!3.09e-18!68;UBERON:0003978!4.96e-17!3;UBERON:0009751!4.96e-17!3;UBERON:0000946!4.96e-17!3;UBERON:0002523!4.96e-17!3;UBERON:0005983!4.96e-17!3;UBERON:0002165!4.96e-17!3;UBERON:0002062!4.96e-17!3;UBERON:0007280!4.96e-17!3;UBERON:0004151!6.46e-17!3;UBERON:0002133!5.07e-12!2;UBERON:0002081!8.17e-12!2;UBERON:0010227!8.17e-12!2;UBERON:0003127!8.72e-11!2;UBERON:0001048!2.06e-10!160;UBERON:0004872!2.94e-09!83;UBERON:0003914!6.81e-09!117;UBERON:0001009!2.14e-08!112;UBERON:0003135!1.40e-07!11;UBERON:0004797!1.52e-07!7;UBERON:0000025!6.14e-07!192;UBERON:0002135!7.49e-07!1;UBERON:0002134!7.90e-07!1;UBERON:0005208!7.90e-07!1;UBERON:0005946!7.90e-07!1;UBERON:0005965!7.90e-07!1;UBERON:0002078!7.90e-07!1;UBERON:0002084!8.34e-07!1;UBERON:0002082!8.34e-07!1;UBERON:0010226!8.34e-07!1
|ontology_enrichment_uberon=UBERON:0007100!3.84e-35!27;UBERON:0000948!3.30e-24!24;UBERON:0005498!3.30e-24!24;UBERON:0004140!3.30e-24!24;UBERON:0009881!3.30e-24!24;UBERON:0004141!3.30e-24!24;UBERON:0003084!3.30e-24!24;UBERON:0007005!3.30e-24!24;UBERON:0004139!3.30e-24!24;UBERON:0004291!3.30e-24!24;UBERON:0007023!2.63e-20!114;UBERON:0003103!3.09e-18!68;UBERON:0003978!4.96e-17!3;UBERON:0009751!4.96e-17!3;UBERON:0000946!4.96e-17!3;UBERON:0002523!4.96e-17!3;UBERON:0005983!4.96e-17!3;UBERON:0002165!4.96e-17!3;UBERON:0002062!4.96e-17!3;UBERON:0007280!4.96e-17!3;UBERON:0004151!6.46e-17!3;UBERON:0002133!5.07e-12!2;UBERON:0002081!8.17e-12!2;UBERON:0010227!8.17e-12!2;UBERON:0003127!8.72e-11!2;UBERON:0001048!2.06e-10!160;UBERON:0004872!2.94e-09!83;UBERON:0003914!6.81e-09!117;UBERON:0001009!2.14e-08!112;UBERON:0003135!1.40e-07!11;UBERON:0004797!1.52e-07!7;UBERON:0000025!6.14e-07!192;UBERON:0002135!7.49e-07!1;UBERON:0002134!7.90e-07!1;UBERON:0005208!7.90e-07!1;UBERON:0005946!7.90e-07!1;UBERON:0005965!7.90e-07!1;UBERON:0002078!7.90e-07!1;UBERON:0002084!8.34e-07!1;UBERON:0002082!8.34e-07!1;UBERON:0010226!8.34e-07!1
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}}
}}

Revision as of 15:31, 26 November 2012


Full id: C2469_heart_left_testis_Cardiac_ovary_pineal_placenta



Phase1 CAGE Peaks

Hg19::chr18:64350315..64350320,-p@chr18:64350315..64350320
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Hg19::chr1:201328328..201328343,-p@chr1:201328328..201328343
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Hg19::chr1:20354880..20354902,+p3@PLA2G5
Hg19::chr1:20355001..20355016,+p2@PLA2G5


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>

Cell Type
Ontology termp-valuen
cardiac fibroblast4.73e-086
cardiac muscle cell9.88e-083
cardiac muscle myoblast9.88e-083
cardiocyte1.14e-0716
Uber Anatomy
Ontology termp-valuen
primary circulatory organ3.84e-3527
heart3.30e-2424
primitive heart tube3.30e-2424
primary heart field3.30e-2424
anterior lateral plate mesoderm3.30e-2424
heart tube3.30e-2424
heart primordium3.30e-2424
cardiac mesoderm3.30e-2424
cardiogenic plate3.30e-2424
heart rudiment3.30e-2424
adult organism2.63e-20114
compound organ3.09e-1868
valve4.96e-173
cardiac mesenchyme4.96e-173
cardial valve4.96e-173
tunica intima4.96e-173
heart layer4.96e-173
endocardium4.96e-173
endocardial cushion4.96e-173
presumptive endocardium4.96e-173
cardiac chamber6.46e-173
atrioventricular valve5.07e-122
cardiac atrium8.17e-122
future cardiac atrium8.17e-122
open tracheal system trachea8.72e-112
primordium2.06e-10160
splanchnic layer of lateral plate mesoderm2.94e-0983
epithelial tube6.81e-09117
circulatory system2.14e-08112
male reproductive organ1.40e-0711
blood vessel layer1.52e-077
tube6.14e-07192
mitral valve7.49e-071
tricuspid valve7.90e-071
right atrium valve7.90e-071
outflow tract of atrium7.90e-071
outflow part of right atrium7.90e-071
right cardiac atrium7.90e-071
heart left ventricle8.34e-071
cardiac ventricle8.34e-071
future cardiac ventricle8.34e-071
Disease
Ontology termp-valuen
heart disease9.08e-122


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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