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Coexpression cluster:C2178


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Full id: C2178_acute_CD14_Macrophage_Dendritic_anaplastic_chronic_mesothelioma

Phase1 CAGE Peaks


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

GO IDGO nameFDR corrected p-value
GO:0047756chondroitin 4-sulfotransferase activity0.00485636911762825
GO:0001537N-acetylgalactosamine 4-O-sulfotransferase activity0.00485636911762825
GO:0030206chondroitin sulfate biosynthetic process0.00485636911762825
GO:0030204chondroitin sulfate metabolic process0.00485636911762825
GO:0050650chondroitin sulfate proteoglycan biosynthetic process0.00485636911762825
GO:0050654chondroitin sulfate proteoglycan metabolic process0.00485636911762825
GO:0006024glycosaminoglycan biosynthetic process0.00755301754465224
GO:0030166proteoglycan biosynthetic process0.00755301754465224
GO:0006023aminoglycan biosynthetic process0.00755301754465224
GO:0006029proteoglycan metabolic process0.0093862161464397
GO:0044272sulfur compound biosynthetic process0.0120176833395542
GO:0030203glycosaminoglycan metabolic process0.0120176833395542
GO:0006022aminoglycan metabolic process0.0120176833395542
GO:0008146sulfotransferase activity0.0120176833395542
GO:0016782transferase activity, transferring sulfur-containing groups0.013371554684495
GO:0006790sulfur metabolic process0.0173822650001481
GO:0016051carbohydrate biosynthetic process0.0262316209486302

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>

Uber Anatomy
Ontology termp-valuen
bone marrow2.92e-1980
bone element2.77e-1786
hematopoietic system1.84e-16102
blood island1.84e-16102
skeletal element6.51e-15101
skeletal system6.51e-15101
hemolymphoid system1.57e-14112
immune system3.20e-13115
musculoskeletal system3.04e-07167

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



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)


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.