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Coexpression cluster:C2030: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004535!3.15e-10!109;UBERON:0001009!8.31e-10!112;UBERON:0005256!3.37e-09!122;UBERON:0003104!4.87e-09!160;UBERON:0009142!4.87e-09!160;UBERON:0002385!1.09e-08!64;UBERON:0001015!1.09e-08!64;UBERON:0000383!1.09e-08!64;UBERON:0001134!1.71e-08!62;UBERON:0002036!1.71e-08!62;UBERON:0003082!1.71e-08!62;UBERON:0007503!6.59e-08!78;UBERON:0002049!1.04e-07!78;UBERON:0007798!1.04e-07!78;UBERON:0000486!4.32e-07!83;UBERON:0001135!5.96e-07!15;UBERON:0002100!8.91e-07!199;UBERON:0002329!9.40e-07!71;UBERON:0003059!9.40e-07!71;UBERON:0007282!9.40e-07!71;UBERON:0004290!9.40e-07!71;UBERON:0009618!9.40e-07!71
|ontology_enrichment_uberon=UBERON:0004535!3.15e-10!109;UBERON:0001009!8.31e-10!112;UBERON:0005256!3.37e-09!122;UBERON:0003104!4.87e-09!160;UBERON:0009142!4.87e-09!160;UBERON:0002385!1.09e-08!64;UBERON:0001015!1.09e-08!64;UBERON:0000383!1.09e-08!64;UBERON:0001134!1.71e-08!62;UBERON:0002036!1.71e-08!62;UBERON:0003082!1.71e-08!62;UBERON:0007503!6.59e-08!78;UBERON:0002049!1.04e-07!78;UBERON:0007798!1.04e-07!78;UBERON:0000486!4.32e-07!83;UBERON:0001135!5.96e-07!15;UBERON:0002100!8.91e-07!199;UBERON:0002329!9.40e-07!71;UBERON:0003059!9.40e-07!71;UBERON:0007282!9.40e-07!71;UBERON:0004290!9.40e-07!71;UBERON:0009618!9.40e-07!71
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}}
}}

Revision as of 15:15, 26 November 2012


Full id: C2030_Neutrophils_Monocytederived_Smooth_CD4_penis_seminal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chrY:10035025..10035038,+p@chrY:10035025..10035038
+
Hg19::chrY:10035343..10035356,+p@chrY:10035343..10035356
+
Hg19::chrY:10035376..10035387,+p@chrY:10035376..10035387
+
Hg19::chrY:10035766..10035786,+p@chrY:10035766..10035786
+
Hg19::chrY:10036084..10036118,+p@chrY:10036084..10036118
+


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 cell8.94e-0959
smooth muscle cell2.48e-0843
smooth muscle myoblast2.48e-0843
mesodermal cell3.41e-08121
muscle cell4.96e-0855
muscle precursor cell1.61e-0758
myoblast1.61e-0758
multi-potent skeletal muscle stem cell1.61e-0758
electrically responsive cell2.44e-0761
electrically active cell2.44e-0761
Uber Anatomy
Ontology termp-valuen
cardiovascular system3.15e-10109
circulatory system8.31e-10112
trunk mesenchyme3.37e-09122
mesenchyme4.87e-09160
entire embryonic mesenchyme4.87e-09160
muscle tissue1.09e-0864
musculature1.09e-0864
musculature of body1.09e-0864
skeletal muscle tissue1.71e-0862
striated muscle tissue1.71e-0862
myotome1.71e-0862
epithelial vesicle6.59e-0878
vasculature1.04e-0778
vascular system1.04e-0778
multilaminar epithelium4.32e-0783
smooth muscle tissue5.96e-0715
trunk8.91e-07199
somite9.40e-0771
presomitic mesoderm9.40e-0771
presumptive segmental plate9.40e-0771
dermomyotome9.40e-0771
trunk paraxial mesoderm9.40e-0771


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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