Coexpression cluster:C2948

Full id: C2948_rhabdomyosarcoma_rectum_Saos2_teratocarcinoma_cerebellum_mesothelioma_gastrointestinal

Phase1 CAGE Peaks

Hg19::chr9:98258815..98258820,-	p@chr9:98258815..98258820 -
Hg19::chr9:98271426..98271454,-	p3@PTCH1
Hg19::chr9:98271460..98271496,-	p@chr9:98271460..98271496 -
Hg19::chr9:98271524..98271555,-	p@chr9:98271524..98271555 -

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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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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	6.83e-26	115
central nervous system	2.56e-25	82
regional part of nervous system	3.11e-25	94
nervous system	3.11e-25	94
neural tube	1.95e-21	57
neural rod	1.95e-21	57
future spinal cord	1.95e-21	57
neural keel	1.95e-21	57
brain	8.00e-20	69
future brain	8.00e-20	69
neurectoderm	4.09e-18	90
regional part of brain	4.57e-18	59
neural plate	9.14e-17	86
presumptive neural plate	9.14e-17	86
regional part of forebrain	2.45e-16	41
forebrain	2.45e-16	41
future forebrain	2.45e-16	41
gray matter	3.96e-16	34
brain grey matter	3.96e-16	34
anterior neural tube	6.46e-16	42
telencephalon	9.04e-16	34
regional part of telencephalon	1.94e-15	33
cerebral hemisphere	5.48e-15	32
ectoderm	3.64e-14	173
presumptive ectoderm	3.64e-14	173
ectoderm-derived structure	4.55e-13	169
cerebral cortex	2.46e-12	25
pallium	2.46e-12	25
pre-chordal neural plate	4.47e-12	61
regional part of cerebral cortex	8.66e-12	22
head	9.70e-12	123
anterior region of body	1.21e-11	129
craniocervical region	1.21e-11	129
neocortex	5.95e-11	20
multi-tissue structure	1.20e-07	347
organ part	3.84e-07	219
posterior neural tube	9.13e-07	15
chordal neural plate	9.13e-07	15

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BATF#10538	3	18.2683513442277	0.000268166010572129	0.00286868687679428
FOSL2#2355	3	12.6976504534213	0.00078756857297571	0.00616958252272803
FOXA1#3169	3	8.31106481203909	0.00274013818210985	0.0150421703864058
FOXA2#3170	3	18.4728478144989	0.000259448418743726	0.00278255631599671
IRF4#3662	3	16.4358845150581	0.000366943139555461	0.00366098343064891
MEF2A#4205	3	14.057423182233	0.000583003885418661	0.00489023715277805
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0435295834755182
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123914703325419
SMARCB1#6598	3	13.6895368358681	0.000630578340937934	0.00518354752847043
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483449593974293
USF2#7392	3	9.7441480388022	0.00171834184841007	0.0107282343559361

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.