Coexpression cluster:C2746

Full id: C2746_mature_breast_colon_uterus_vagina_hippocampus_smooth

Phase1 CAGE Peaks

Hg19::chr3:64253787..64253799,-	p5@PRICKLE2
Hg19::chr3:64253805..64253834,-	p2@PRICKLE2
Hg19::chr3:64253837..64253863,-	p1@PRICKLE2
Hg19::chr3:64253867..64253883,-	p3@PRICKLE2

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><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	2.84e-15	180
muscle precursor cell	3.68e-08	57
myoblast	3.68e-08	57
multi-potent skeletal muscle stem cell	3.68e-08	57
fat cell	3.87e-08	15
muscle cell	6.06e-08	54
contractile cell	9.54e-08	59
fibroblast	2.17e-07	75
electrically responsive cell	8.16e-07	60
electrically active cell	8.16e-07	60

Uber Anatomy

Ontology term	p-value	n
organism subdivision	9.84e-33	365
cell layer	6.04e-26	312
adult organism	7.84e-26	115
head	8.01e-26	123
brain	1.14e-25	69
future brain	1.14e-25	69
epithelium	1.43e-25	309
neural plate	5.24e-25	86
presumptive neural plate	5.24e-25	86
central nervous system	5.93e-25	82
anterior region of body	7.55e-25	129
craniocervical region	7.55e-25	129
ectoderm-derived structure	8.24e-25	169
multi-tissue structure	1.00e-24	347
regional part of brain	8.63e-24	59
neural tube	3.22e-23	57
neural rod	3.22e-23	57
future spinal cord	3.22e-23	57
neural keel	3.22e-23	57
ectoderm	5.31e-23	173
presumptive ectoderm	5.31e-23	173
neurectoderm	2.89e-22	90
regional part of nervous system	4.63e-21	94
nervous system	4.63e-21	94
pre-chordal neural plate	3.74e-20	61
anterior neural tube	3.83e-20	42
multi-cellular organism	1.24e-19	659
regional part of forebrain	1.87e-19	41
forebrain	1.87e-19	41
future forebrain	1.87e-19	41
anatomical cluster	3.07e-19	286
anatomical conduit	3.95e-19	241
tube	2.77e-17	194
gray matter	3.82e-17	34
brain grey matter	3.82e-17	34
telencephalon	8.60e-17	34
cerebral hemisphere	1.00e-16	32
regional part of telencephalon	3.18e-16	33
anatomical system	8.14e-16	625
anatomical group	1.53e-15	626
embryo	3.90e-14	612
embryonic structure	1.01e-13	605
developing anatomical structure	1.01e-13	605
cerebral cortex	1.88e-13	25
pallium	1.88e-13	25
germ layer	2.45e-13	604
embryonic tissue	2.45e-13	604
presumptive structure	2.45e-13	604
epiblast (generic)	2.45e-13	604
regional part of cerebral cortex	1.27e-12	22
somite	8.37e-12	83
paraxial mesoderm	8.37e-12	83
presomitic mesoderm	8.37e-12	83
presumptive segmental plate	8.37e-12	83
trunk paraxial mesoderm	8.37e-12	83
presumptive paraxial mesoderm	8.37e-12	83
organ	1.83e-11	511
neocortex	2.48e-11	20
organ part	1.35e-10	219
trunk mesenchyme	1.80e-10	143
dermomyotome	2.41e-10	70
muscle tissue	1.69e-09	63
musculature	1.69e-09	63
musculature of body	1.69e-09	63
multilaminar epithelium	1.70e-09	82
tissue	3.78e-09	787
skeletal muscle tissue	6.24e-09	61
striated muscle tissue	6.24e-09	61
myotome	6.24e-09	61
trunk	1.22e-07	216

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
NANOG#79923	4	29.2447784810127	1.36586687657858e-06	5.34669305558436e-05
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322894738686762

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.