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Coexpression cluster:C4099

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Full id: C4099_malignant_Reticulocytes_rectal_neuroblastoma_choriocarcinoma_small_hepatocellular



Phase1 CAGE Peaks

Hg19::chr22:38201228..38201242,+p1@H1F0
Hg19::chr22:38201615..38201680,-p@chr22:38201615..38201680
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Hg19::chr22:38201945..38202027,-p@chr22:38201945..38202027
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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
epithelial cell6.22e-15253
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.34e-13160
endoderm3.34e-13160
presumptive endoderm3.34e-13160
multi-cellular organism1.79e-11656
organ system subdivision6.23e-11223
digestive system9.30e-11145
digestive tract9.30e-11145
primitive gut9.30e-11145
immaterial anatomical entity1.06e-09117
subdivision of digestive tract1.77e-09118
trunk region element4.08e-09101
anatomical cluster8.10e-08373
organ part9.54e-08218
organ1.62e-07503
subdivision of trunk3.92e-07112
anatomical space7.61e-0795
Disease
Ontology termp-valuen
cell type cancer9.66e-23143
carcinoma1.50e-14106
cancer1.08e-10235
disease of cellular proliferation3.89e-10239
germ cell and embryonal cancer1.72e-0822
germ cell cancer1.72e-0822


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
TAF7#6879311.43306940492390.0006690181981945830.00544086525473011



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.