Coexpression cluster:C4474

Full id: C4474_occipital_medial_Smooth_insula_Mesenchymal_hippocampus_parietal

Phase1 CAGE Peaks

Hg19::chr5:143584901..143584987,+	p1@KCTD16
Hg19::chr5:143584993..143585004,+	p4@KCTD16
Hg19::chr5:143585025..143585036,+	p6@KCTD16

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
vascular associated smooth muscle cell	7.21e-14	32
smooth muscle cell	2.07e-13	42
smooth muscle myoblast	2.07e-13	42
non-terminally differentiated cell	4.18e-13	180
muscle cell	1.21e-09	54
muscle precursor cell	1.29e-09	57
myoblast	1.29e-09	57
multi-potent skeletal muscle stem cell	1.29e-09	57
electrically responsive cell	3.77e-09	60
electrically active cell	3.77e-09	60
contractile cell	4.44e-08	59
fibroblast	2.01e-07	75

Uber Anatomy

Ontology term	p-value	n
neural tube	7.91e-24	57
neural rod	7.91e-24	57
future spinal cord	7.91e-24	57
neural keel	7.91e-24	57
tube	1.94e-23	194
regional part of forebrain	4.69e-22	41
forebrain	4.69e-22	41
future forebrain	4.69e-22	41
regional part of brain	3.32e-21	59
anterior neural tube	4.56e-21	42
neural plate	4.84e-21	86
presumptive neural plate	4.84e-21	86
cerebral hemisphere	2.51e-20	32
telencephalon	2.86e-20	34
central nervous system	4.39e-20	82
gray matter	5.77e-20	34
brain grey matter	5.77e-20	34
regional part of nervous system	8.94e-20	94
nervous system	8.94e-20	94
regional part of telencephalon	1.68e-19	33
neurectoderm	2.37e-19	90
brain	4.60e-19	69
future brain	4.60e-19	69
regional part of cerebral cortex	1.24e-18	22
pre-chordal neural plate	5.42e-18	61
neocortex	3.53e-17	20
epithelium	4.04e-16	309
anatomical conduit	5.22e-16	241
cerebral cortex	9.47e-16	25
pallium	9.47e-16	25
cell layer	1.95e-15	312
artery	2.22e-15	42
arterial blood vessel	2.22e-15	42
arterial system	2.22e-15	42
anatomical cluster	3.26e-15	286
organism subdivision	1.19e-14	365
adult organism	2.60e-13	115
systemic artery	6.25e-13	33
systemic arterial system	6.25e-13	33
head	4.38e-12	123
anterior region of body	1.09e-11	129
craniocervical region	1.09e-11	129
splanchnic layer of lateral plate mesoderm	1.81e-11	84
multi-tissue structure	2.75e-11	347
blood vessel	9.35e-11	60
epithelial tube open at both ends	9.35e-11	60
blood vasculature	9.35e-11	60
vascular cord	9.35e-11	60
skeletal muscle tissue	3.27e-10	61
striated muscle tissue	3.27e-10	61
myotome	3.27e-10	61
muscle tissue	9.52e-10	63
musculature	9.52e-10	63
musculature of body	9.52e-10	63
ectoderm-derived structure	1.36e-08	169
vessel	4.37e-08	69
vasculature	4.49e-08	79
vascular system	4.49e-08	79
ectoderm	4.88e-08	173
presumptive ectoderm	4.88e-08	173
multi-cellular organism	5.52e-08	659
temporal lobe	3.21e-07	7
dermomyotome	5.99e-07	70
somite	6.42e-07	83
paraxial mesoderm	6.42e-07	83
presomitic mesoderm	6.42e-07	83
presumptive segmental plate	6.42e-07	83
trunk paraxial mesoderm	6.42e-07	83
presumptive paraxial mesoderm	6.42e-07	83
organ part	9.06e-07	219
epithelial tube	9.32e-07	118
aorta	9.56e-07	21
aortic system	9.56e-07	21

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115624787947107

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.