Coexpression cluster:C4747

Full id: C4747_Mast_retinoblastoma_testis_adrenal_epidermoid_prostate_chronic

Phase1 CAGE Peaks

Hg19::chr8:30770484..30770501,-	p@chr8:30770484..30770501 -
Hg19::chr8:30770514..30770529,-	p@chr8:30770514..30770529 -
Hg19::chr8:30770534..30770545,-	p@chr8:30770534..30770545 -

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
neurectoderm	5.62e-17	90
neural plate	6.36e-17	86
presumptive neural plate	6.36e-17	86
neural tube	4.17e-16	57
neural rod	4.17e-16	57
future spinal cord	4.17e-16	57
neural keel	4.17e-16	57
central nervous system	2.76e-15	82
regional part of nervous system	2.84e-15	94
nervous system	2.84e-15	94
regional part of brain	3.37e-14	59
brain	1.58e-13	69
future brain	1.58e-13	69
regional part of forebrain	6.02e-13	41
forebrain	6.02e-13	41
future forebrain	6.02e-13	41
adult organism	7.20e-13	115
anterior neural tube	2.12e-12	42
pre-chordal neural plate	5.03e-12	61
head	1.21e-11	123
gray matter	7.40e-11	34
brain grey matter	7.40e-11	34
anterior region of body	9.77e-11	129
craniocervical region	9.77e-11	129
telencephalon	1.14e-10	34
regional part of telencephalon	3.12e-10	33
cerebral hemisphere	3.55e-10	32
ectoderm	5.73e-09	173
presumptive ectoderm	5.73e-09	173
ectoderm-derived structure	9.52e-09	169
cell layer	5.36e-08	312
epithelium	9.95e-08	309
cerebral cortex	3.34e-07	25
pallium	3.34e-07	25

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191270373659437
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281474127791504
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172410265591555
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324510033990273
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322651876900142
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109279912796364
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128781293031738
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187476106364838
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00200297221049566
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246791893111305
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00473733889486397
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00669036076012733
REST#5978	3	9.65002871612802	0.00111263624711459	0.00771597722525901
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000360165862737716
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310999767804257
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191260933280064
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0141007268225583

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.