Coexpression cluster:C459

Full id: C459_diffuse_acute_testicular_iPS_CD14_Renal_chronic

Phase1 CAGE Peaks

Hg19::chr10:112360803..112360817,+	p@chr10:112360803..112360817 +
Hg19::chr10:70098368..70098404,+	p3@HNRNPH3
Hg19::chr1:245019788..245019803,-	p@chr1:245019788..245019803 -
Hg19::chr1:245022599..245022657,-	p7@HNRNPU
Hg19::chr1:44588180..44588202,-	p1@ENST00000402743
Hg19::chr6:114267231..114267258,-	p@chr6:114267231..114267258 -
Hg19::chr7:26233209..26233239,-	p@chr7:26233209..26233239 -
Hg19::chr7:26233242..26233284,-	p@chr7:26233242..26233284 -
Hg19::chr7:26233292..26233320,-	p@chr7:26233292..26233320 -
Hg19::chr7:26235486..26235540,-	p@chr7:26235486..26235540 -
Hg19::chr7:26236054..26236075,-	p@chr7:26236054..26236075 -
Hg19::chr7:26236076..26236108,-	p@chr7:26236076..26236108 -
Hg19::chr7:26236464..26236483,-	p3@HNRNPA2B1
Hg19::chr7:26236559..26236570,-	p9@HNRNPA2B1
Hg19::chr7:26236592..26236600,-	p11@HNRNPA2B1
Hg19::chr7:26236610..26236626,-	p5@HNRNPA2B1
Hg19::chr7:26236630..26236642,-	p8@HNRNPA2B1
Hg19::chr7:26236955..26236980,-	p6@HNRNPA2B1
Hg19::chr7:26236987..26237030,-	p4@HNRNPA2B1
Hg19::chr7:26237039..26237051,-	p@chr7:26237039..26237051 -
Hg19::chr7:26237272..26237323,-	p@chr7:26237272..26237323 -

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:0030530	heterogeneous nuclear ribonucleoprotein complex	1.45832616951182e-05
GO:0005681	spliceosome	0.000457085172934245
GO:0008380	RNA splicing	0.000800649661692765
GO:0006397	mRNA processing	0.000884717876170506
GO:0016071	mRNA metabolic process	0.00111158767673731
GO:0043047	single-stranded telomeric DNA binding	0.00187294831574558
GO:0006396	RNA processing	0.00187294831574558
GO:0003723	RNA binding	0.00539548910907402
GO:0042162	telomeric DNA binding	0.00539548910907402
GO:0044428	nuclear part	0.00560587338291255
GO:0030529	ribonucleoprotein complex	0.00560587338291255
GO:0003697	single-stranded DNA binding	0.0150951373577981
GO:0000375	RNA splicing, via transesterification reactions	0.0150951373577981
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0150951373577981
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0150951373577981
GO:0050658	RNA transport	0.0156575469235196
GO:0051236	establishment of RNA localization	0.0156575469235196
GO:0050657	nucleic acid transport	0.0156575469235196
GO:0006403	RNA localization	0.0156575469235196
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0168118700284401
GO:0009986	cell surface	0.0227705399221662
GO:0043566	structure-specific DNA binding	0.0233472040861499
GO:0003677	DNA binding	0.0254627520372707
GO:0032991	macromolecular complex	0.0299326331208392
GO:0044446	intracellular organelle part	0.0304654080166691
GO:0044422	organelle part	0.0304654080166691
GO:0016070	RNA metabolic process	0.0304654080166691
GO:0000166	nucleotide binding	0.0309391045519627
GO:0010467	gene expression	0.0488748993612867

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

Uber Anatomy

Ontology term	p-value	n

Disease

Ontology term	p-value	n

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)
{{{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

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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.