Coexpression cluster:C3300

Full id: C3300_acute_lymphoma_chronic_giant_Fibroblast_hereditary_diffuse

Phase1 CAGE Peaks

Hg19::chr12:56498312..56498413,+	p1@PA2G4
Hg19::chr1:19578280..19578334,+	p1@MRTO4
Hg19::chr5:175815565..175815615,-	p1@NOP16

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0042254	ribosome biogenesis and assembly	0.000846401070932352
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.00208896775368931
GO:0004239	methionyl aminopeptidase activity	0.0188359938245719
GO:0050897	cobalt ion binding	0.0211886214040835
GO:0006996	organelle organization and biogenesis	0.0322637551551224
GO:0006364	rRNA processing	0.0488047959039513
GO:0016072	rRNA metabolic process	0.0488047959039513
GO:0004177	aminopeptidase activity	0.0488047959039513

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>

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Cell Type

Ontology term	p-value	n
epithelial cell	7.29e-29	254
animal cell	2.55e-27	679
eukaryotic cell	2.55e-27	679
embryonic cell	1.35e-19	248
native cell	4.59e-16	722
squamous epithelial cell	1.26e-11	62
somatic cell	1.85e-08	591
mesodermal cell	3.74e-08	119
non-terminally differentiated cell	5.17e-07	180

Uber Anatomy

Ontology term	p-value	n
mesenchyme	2.15e-11	238
entire embryonic mesenchyme	2.15e-11	238
trunk	6.38e-08	216
segment of respiratory tract	1.96e-07	46
respiratory primordium	4.12e-07	38
endoderm of foregut	4.12e-07	38
larynx	4.48e-07	9

Disease

Ontology term	p-value	n
disease of cellular proliferation	7.15e-33	239
cancer	7.44e-33	235
hematologic cancer	6.83e-19	51
immune system cancer	6.83e-19	51
organ system cancer	6.83e-17	137
leukemia	4.38e-15	39
cell type cancer	6.12e-15	143
carcinoma	9.95e-14	106
myeloid leukemia	9.93e-13	31

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

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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

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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

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This analysis result is provided for C0 - C305 clusters.