Coexpression cluster:C3706

Full id: C3706_temporal_duodenum_occipital_Neural_mucinous_parietal_Neurons

Phase1 CAGE Peaks

Hg19::chr18:12657866..12657958,-	p2@SPIRE1
Hg19::chr18:12657964..12657987,-	p3@SPIRE1
Hg19::chr18:12657988..12658128,-	p1@SPIRE1

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
neural tube	5.22e-27	57
neural rod	5.22e-27	57
future spinal cord	5.22e-27	57
neural keel	5.22e-27	57
regional part of nervous system	1.14e-26	94
nervous system	1.14e-26	94
central nervous system	5.69e-26	82
regional part of brain	2.89e-23	59
brain	2.93e-23	69
future brain	2.93e-23	69
anatomical system	1.43e-22	625
neural plate	1.67e-22	86
presumptive neural plate	1.67e-22	86
anatomical group	2.33e-22	626
anterior neural tube	2.56e-22	42
regional part of forebrain	4.47e-22	41
forebrain	4.47e-22	41
future forebrain	4.47e-22	41
multi-cellular organism	3.16e-21	659
organ	1.10e-20	511
neurectoderm	3.94e-20	90
telencephalon	2.73e-19	34
gray matter	2.85e-19	34
brain grey matter	2.85e-19	34
regional part of telencephalon	1.27e-18	33
ectoderm-derived structure	2.48e-18	169
cerebral hemisphere	4.39e-18	32
embryonic structure	4.79e-18	605
developing anatomical structure	4.79e-18	605
germ layer	5.75e-18	604
embryonic tissue	5.75e-18	604
presumptive structure	5.75e-18	604
epiblast (generic)	5.75e-18	604
embryo	4.13e-17	612
ectoderm	5.77e-17	173
presumptive ectoderm	5.77e-17	173
adult organism	1.16e-16	115
pre-chordal neural plate	1.97e-16	61
head	2.88e-16	123
cerebral cortex	2.60e-14	25
pallium	2.60e-14	25
anterior region of body	4.82e-14	129
craniocervical region	4.82e-14	129
regional part of cerebral cortex	6.54e-14	22
tube	5.32e-13	194
neocortex	8.38e-13	20
anatomical conduit	1.25e-12	241
organism subdivision	1.32e-10	365
anatomical cluster	1.54e-10	286
epithelium	2.40e-09	309
cell layer	2.51e-09	312
multi-tissue structure	7.79e-07	347

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279236986307183
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325053098650114
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321895156920866
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461883804448639
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156650192206468
REST#5978	3	9.65002871612802	0.00111263624711459	0.00766963349035712
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.0024815130206037
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00615557694777458
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329084417485298
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.014007528692075

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.