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Coexpression cluster:C4054: Difference between revisions

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|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222929074722192
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222929074722192
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}}
}}

Revision as of 16:31, 26 November 2012


Full id: C4054_Osteoblast_Fibroblast_leiomyoblastoma_meningioma_Smooth_salivary_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr20:57089878..57089902,-p4@APCDD1L
Hg19::chr20:57089913..57089929,-p5@APCDD1L
Hg19::chr20:57089934..57089974,-p2@APCDD1L


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>


Uber Anatomy
Ontology termp-valuen
somite1.13e-2171
presomitic mesoderm1.13e-2171
presumptive segmental plate1.13e-2171
dermomyotome1.13e-2171
trunk paraxial mesoderm1.13e-2171
paraxial mesoderm4.30e-2172
presumptive paraxial mesoderm4.30e-2172
epithelial vesicle4.55e-2178
dense mesenchyme tissue1.58e-2073
muscle tissue2.11e-1964
musculature2.11e-1964
musculature of body2.11e-1964
skeletal muscle tissue1.33e-1862
striated muscle tissue1.33e-1862
myotome1.33e-1862
multilaminar epithelium3.48e-1883
mesenchyme6.87e-16160
entire embryonic mesenchyme6.87e-16160
trunk mesenchyme7.77e-13122
artery9.14e-1042
arterial blood vessel9.14e-1042
arterial system9.14e-1042
systemic artery1.80e-0933
systemic arterial system1.80e-0933
splanchnic layer of lateral plate mesoderm6.16e-0983
unilaminar epithelium1.33e-08148
vasculature1.52e-0878
vascular system1.52e-0878
epithelial tube2.94e-08117
epithelial tube open at both ends3.64e-0859
blood vessel3.64e-0859
blood vasculature3.64e-0859
vascular cord3.64e-0859
multi-tissue structure9.19e-08342
cardiovascular system2.02e-07109
mesoderm2.26e-07315
mesoderm-derived structure2.26e-07315
presumptive mesoderm2.26e-07315
vessel4.28e-0768
organism subdivision6.55e-07264
trunk7.33e-07199
circulatory system7.54e-07112
Disease
Ontology termp-valuen
ovarian cancer5.79e-0714


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)

{{{tfbs_overrepresentation_jaspar}}}



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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
SUZ12#23512350.11578091106297.93834897779404e-060.000222929074722192



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.