Coexpression cluster:C4447

Full id: C4447_mesothelioma_Wilms_leiomyoblastoma_large_endometrial_serous_merkel

Phase1 CAGE Peaks

Hg19::chr5:107007726..107007737,-	p@chr5:107007726..107007737 -
Hg19::chr5:107007827..107007856,-	p@chr5:107007827..107007856 -
Hg19::chr5:107007859..107007895,-	p@chr5:107007859..107007895 -

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

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Cell Type

Ontology term	p-value	n
epithelial cell	6.14e-14	254

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	4.14e-22	347
ectoderm	4.28e-20	173
presumptive ectoderm	4.28e-20	173
ectoderm-derived structure	3.09e-19	169
organ part	1.89e-17	219
neurectoderm	3.48e-17	90
head	6.82e-17	123
anterior region of body	1.13e-16	129
craniocervical region	1.13e-16	129
anatomical cluster	1.19e-16	286
neural plate	2.29e-16	86
presumptive neural plate	2.29e-16	86
organism subdivision	4.36e-15	365
pre-chordal neural plate	1.01e-14	61
multi-cellular organism	4.11e-14	659
embryo	4.43e-14	612
cell layer	1.89e-13	312
epithelium	2.85e-13	309
regional part of nervous system	4.32e-13	94
nervous system	4.32e-13	94
embryonic structure	2.04e-12	605
developing anatomical structure	2.04e-12	605
central nervous system	3.62e-12	82
germ layer	4.53e-12	604
embryonic tissue	4.53e-12	604
presumptive structure	4.53e-12	604
epiblast (generic)	4.53e-12	604
brain	9.65e-12	69
future brain	9.65e-12	69
anatomical system	2.82e-11	625
anatomical group	3.22e-11	626
regional part of brain	3.44e-11	59
adult organism	4.72e-11	115
neocortex	5.51e-11	20
organ	1.68e-10	511
cerebral hemisphere	4.57e-10	32
anterior neural tube	4.88e-10	42
anatomical conduit	5.00e-10	241
regional part of cerebral cortex	5.73e-10	22
regional part of forebrain	7.28e-10	41
forebrain	7.28e-10	41
future forebrain	7.28e-10	41
telencephalon	1.58e-09	34
neural tube	2.42e-09	57
neural rod	2.42e-09	57
future spinal cord	2.42e-09	57
neural keel	2.42e-09	57
regional part of telencephalon	5.08e-09	33
gray matter	6.63e-09	34
brain grey matter	6.63e-09	34
cerebral cortex	1.71e-08	25
pallium	1.71e-08	25
kidney	3.78e-08	27
kidney mesenchyme	3.78e-08	27
kidney rudiment	3.78e-08	27
kidney field	3.78e-08	27
cavitated compound organ	4.11e-08	32
compound organ	1.31e-07	69
subdivision of head	1.49e-07	48
trunk region element	1.85e-07	107
tube	4.29e-07	194
sense organ	4.83e-07	23

Disease

Ontology term	p-value	n
cell type cancer	1.09e-10	143
carcinoma	8.33e-10	106

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326989656853291
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321972817732441
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00392892686326598
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187205239326168
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295605684743296
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109864547153651

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.