Coexpression cluster:C4147

Full id: C4147_extraskeletal_occipital_small_brain_medial_temporal_insula

Phase1 CAGE Peaks

Hg19::chr2:175869890..175869933,-	p6@CHN1
Hg19::chr2:175869936..175869949,-	p14@CHN1
Hg19::chr2:175869984..175869996,-	p9@CHN1

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
neural cell	1.19e-07	25

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	5.47e-32	94
nervous system	5.47e-32	94
central nervous system	1.94e-31	82
neural tube	2.06e-26	57
neural rod	2.06e-26	57
future spinal cord	2.06e-26	57
neural keel	2.06e-26	57
neurectoderm	4.70e-26	90
neural plate	7.85e-26	86
presumptive neural plate	7.85e-26	86
brain	9.52e-26	69
future brain	9.52e-26	69
adult organism	2.64e-25	115
anterior neural tube	3.23e-25	42
regional part of forebrain	1.01e-24	41
forebrain	1.01e-24	41
future forebrain	1.01e-24	41
telencephalon	1.30e-23	34
gray matter	2.70e-23	34
brain grey matter	2.70e-23	34
cerebral hemisphere	3.67e-23	32
regional part of telencephalon	7.34e-23	33
regional part of brain	9.03e-23	59
pre-chordal neural plate	1.58e-22	61
anatomical cluster	1.12e-20	286
cerebral cortex	7.81e-19	25
pallium	7.81e-19	25
head	8.59e-19	123
ectoderm	1.69e-18	173
presumptive ectoderm	1.69e-18	173
anterior region of body	3.01e-18	129
craniocervical region	3.01e-18	129
anatomical conduit	4.63e-18	241
ectoderm-derived structure	4.83e-18	169
regional part of cerebral cortex	4.35e-17	22
tube	2.09e-16	194
neocortex	7.40e-16	20
cell layer	2.27e-14	312
epithelium	3.42e-14	309
organ part	5.98e-14	219
multi-tissue structure	6.77e-14	347
organism subdivision	4.91e-13	365
multi-cellular organism	8.28e-12	659
anatomical group	9.68e-10	626
anatomical system	1.38e-09	625
embryo	4.28e-09	612
embryonic structure	2.51e-07	605
developing anatomical structure	2.51e-07	605
germ layer	3.80e-07	604
embryonic tissue	3.80e-07	604
presumptive structure	3.80e-07	604
epiblast (generic)	3.80e-07	604
organ	8.60e-07	511

Disease

Ontology term	p-value	n
cell type cancer	1.50e-09	143
carcinoma	2.40e-08	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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280113675321078
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326180963670715
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323077346596606
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108899624435329
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295117886583654
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000738442039317454
SREBF1#6720	3	47.0058494404883	9.62099323994382e-06	0.000254962424000632
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00544213658394299
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00616935603361499
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330057711970017
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109640163705534

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.