Coexpression cluster:C1884

Full id: C1884_small_parietal_temporal_duodenum_occipital_rhabdomyosarcoma_acute

Phase1 CAGE Peaks

Hg19::chr2:172949484..172949522,+	p1@DLX1
Hg19::chr2:172949532..172949541,+	p6@DLX1
Hg19::chr2:172950053..172950081,-	p@chr2:172950053..172950081 -
Hg19::chr2:172950227..172950249,+	p2@DLX1
Hg19::chr2:172967621..172967637,-	p1@DLX2

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:0043565	sequence-specific DNA binding	0.0329591072552472
GO:0003727	single-stranded RNA binding	0.0329591072552472
GO:0003700	transcription factor activity	0.0363204124571804
GO:0007275	multicellular organismal development	0.0380691710092592
GO:0003682	chromatin binding	0.0380691710092592
GO:0007420	brain development	0.0380691710092592
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0380691710092592
GO:0032502	developmental process	0.0380691710092592
GO:0006355	regulation of transcription, DNA-dependent	0.0380691710092592
GO:0006351	transcription, DNA-dependent	0.0380691710092592
GO:0032774	RNA biosynthetic process	0.0380691710092592
GO:0003677	DNA binding	0.0380691710092592
GO:0045449	regulation of transcription	0.0380691710092592
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0380691710092592
GO:0006350	transcription	0.0380691710092592
GO:0032501	multicellular organismal process	0.0380691710092592
GO:0010468	regulation of gene expression	0.0380691710092592
GO:0045893	positive regulation of transcription, DNA-dependent	0.0380691710092592
GO:0031323	regulation of cellular metabolic process	0.0380691710092592
GO:0007417	central nervous system development	0.0380691710092592
GO:0019222	regulation of metabolic process	0.0380691710092592
GO:0016070	RNA metabolic process	0.0380691710092592
GO:0045941	positive regulation of transcription	0.0395310782558458
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0395310782558458
GO:0031325	positive regulation of cellular metabolic process	0.0478758800868458
GO:0009893	positive regulation of metabolic process	0.0492946969816967

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
cerebral hemisphere	2.32e-13	32
telencephalon	2.99e-12	34
cerebral cortex	6.49e-12	25
pallium	6.49e-12	25
regional part of cerebral cortex	7.75e-12	22
regional part of telencephalon	8.88e-12	33
neocortex	3.63e-11	20
gray matter	4.44e-10	34
brain grey matter	4.44e-10	34
regional part of forebrain	2.35e-09	41
forebrain	2.35e-09	41
future forebrain	2.35e-09	41
anterior neural tube	5.98e-09	42
ectoderm	2.77e-07	173
presumptive ectoderm	2.77e-07	173

Disease

Ontology term	p-value	n
cancer	1.46e-24	235
disease of cellular proliferation	1.61e-24	239
cell type cancer	1.62e-19	143
carcinoma	7.55e-12	106
organ system cancer	8.48e-08	137
disease of anatomical entity	7.47e-07	39

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.