Coexpression cluster:C4835

Full id: C4835_rhabdomyosarcoma_rectum_colon_stomach_duodenum_small_testis

Phase1 CAGE Peaks

Hg19::chr9:98279050..98279078,-	p4@PTCH1
Hg19::chr9:98279086..98279094,-	p15@PTCH1
Hg19::chr9:98279099..98279113,-	p11@PTCH1

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	8.86e-27	115
neural tube	3.70e-24	57
neural rod	3.70e-24	57
future spinal cord	3.70e-24	57
neural keel	3.70e-24	57
central nervous system	2.38e-23	82
regional part of nervous system	1.84e-22	94
nervous system	1.84e-22	94
neurectoderm	4.04e-19	90
regional part of brain	1.26e-18	59
brain	5.51e-18	69
future brain	5.51e-18	69
neural plate	1.28e-17	86
presumptive neural plate	1.28e-17	86
regional part of forebrain	1.20e-16	41
forebrain	1.20e-16	41
future forebrain	1.20e-16	41
gray matter	4.28e-16	34
brain grey matter	4.28e-16	34
anterior neural tube	4.89e-16	42
telencephalon	7.27e-16	34
regional part of telencephalon	3.64e-15	33
cerebral hemisphere	1.50e-14	32
regional part of cerebral cortex	2.12e-14	22
neocortex	2.32e-14	20
cerebral cortex	4.79e-12	25
pallium	4.79e-12	25
ectoderm	2.50e-11	173
presumptive ectoderm	2.50e-11	173
ectoderm-derived structure	2.87e-10	169
pre-chordal neural plate	4.25e-10	61
posterior neural tube	1.47e-09	15
chordal neural plate	1.47e-09	15
temporal lobe	2.08e-09	7
head	3.92e-08	123
male reproductive organ	5.67e-08	11
anterior region of body	9.90e-08	129
craniocervical region	9.90e-08	129
testis	3.60e-07	8
segmental subdivision of hindbrain	8.23e-07	12
hindbrain	8.23e-07	12
presumptive hindbrain	8.23e-07	12

Disease

Ontology term	p-value	n
germ cell and embryonal cancer	2.06e-07	22
germ cell cancer	2.06e-07	22

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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00130114615933376
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191430917689554
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00663248301911973
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324803200681101
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465427832539064
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00584975653595772
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107787727537765
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187629945907639
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000723595064960936
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191396297722793
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00423494840229661

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.