Coexpression cluster:C1620

Full id: C1620_spinal_occipital_optic_diencephalon_substantia_brain_corpus

Phase1 CAGE Peaks

Hg19::chr11:125366047..125366076,-	p5@FEZ1
Hg19::chr11:125366089..125366207,-	p1@FEZ1
Hg19::chr17:40126302..40126313,+	p6@BC148241
Hg19::chr17:42984454..42984463,-	p37@GFAP
Hg19::chr4:83551834..83551855,-	p@chr4:83551834..83551855 -

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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GO ID	GO name	FDR corrected p-value
GO:0043015	gamma-tubulin binding	0.0207887046966037
GO:0044430	cytoskeletal part	0.0207887046966037
GO:0005856	cytoskeleton	0.0322259237004165
GO:0007411	axon guidance	0.0322259237004165
GO:0015631	tubulin binding	0.0322259237004165
GO:0005200	structural constituent of cytoskeleton	0.0322259237004165
GO:0007409	axonogenesis	0.0322259237004165
GO:0048667	neuron morphogenesis during differentiation	0.0322259237004165
GO:0048812	neurite morphogenesis	0.0322259237004165
GO:0043232	intracellular non-membrane-bound organelle	0.0322259237004165
GO:0043228	non-membrane-bound organelle	0.0322259237004165
GO:0000904	cellular morphogenesis during differentiation	0.0322259237004165
GO:0005813	centrosome	0.0322259237004165
GO:0031175	neurite development	0.0322259237004165
GO:0005815	microtubule organizing center	0.0322259237004165
GO:0048666	neuron development	0.0322259237004165
GO:0032990	cell part morphogenesis	0.0323941803318015
GO:0048858	cell projection morphogenesis	0.0323941803318015
GO:0030030	cell projection organization and biogenesis	0.0323941803318015
GO:0030182	neuron differentiation	0.0323941803318015
GO:0016477	cell migration	0.0323941803318015
GO:0045111	intermediate filament cytoskeleton	0.0323941803318015
GO:0005882	intermediate filament	0.0323941803318015
GO:0048699	generation of neurons	0.0323941803318015
GO:0044446	intracellular organelle part	0.0323941803318015
GO:0044422	organelle part	0.0323941803318015
GO:0022008	neurogenesis	0.0324376738613004
GO:0051674	localization of cell	0.0440692668892321
GO:0006928	cell motility	0.0440692668892321

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	5.67e-19	180
embryonic cell	8.34e-17	248
electrically responsive cell	1.44e-12	60
electrically active cell	1.44e-12	60
contractile cell	2.14e-12	59
mesodermal cell	8.74e-12	119
smooth muscle cell	1.26e-11	42
smooth muscle myoblast	1.26e-11	42
muscle cell	1.44e-11	54
muscle precursor cell	3.49e-11	57
myoblast	3.49e-11	57
multi-potent skeletal muscle stem cell	3.49e-11	57
vascular associated smooth muscle cell	8.79e-11	32
ectodermal cell	2.66e-08	71

Uber Anatomy

Ontology term	p-value	n
cell layer	2.51e-33	312
epithelium	3.81e-33	309
anatomical conduit	3.78e-31	241
neural tube	9.29e-30	57
neural rod	9.29e-30	57
future spinal cord	9.29e-30	57
neural keel	9.29e-30	57
tube	5.56e-29	194
central nervous system	1.34e-28	82
regional part of brain	4.25e-27	59
anatomical cluster	1.02e-26	286
regional part of nervous system	3.05e-26	94
nervous system	3.05e-26	94
neural plate	4.37e-26	86
presumptive neural plate	4.37e-26	86
ectoderm-derived structure	2.50e-25	169
head	1.91e-24	123
brain	2.87e-24	69
future brain	2.87e-24	69
ectoderm	4.64e-24	173
presumptive ectoderm	4.64e-24	173
neurectoderm	5.31e-24	90
organism subdivision	4.56e-23	365
anterior region of body	6.50e-22	129
craniocervical region	6.50e-22	129
regional part of forebrain	3.82e-21	41
forebrain	3.82e-21	41
future forebrain	3.82e-21	41
gray matter	5.96e-21	34
brain grey matter	5.96e-21	34
telencephalon	6.43e-21	34
anterior neural tube	7.01e-21	42
regional part of telencephalon	2.63e-20	33
cerebral hemisphere	1.47e-19	32
pre-chordal neural plate	3.74e-18	61
vessel	1.55e-17	69
vasculature	1.93e-17	79
vascular system	1.93e-17	79
blood vessel	1.48e-16	60
epithelial tube open at both ends	1.48e-16	60
blood vasculature	1.48e-16	60
vascular cord	1.48e-16	60
splanchnic layer of lateral plate mesoderm	2.32e-16	84
multi-tissue structure	4.59e-16	347
multi-cellular organism	1.18e-15	659
cerebral cortex	2.16e-15	25
pallium	2.16e-15	25
artery	9.85e-15	42
arterial blood vessel	9.85e-15	42
arterial system	9.85e-15	42
anatomical system	2.42e-14	625
anatomical group	3.16e-14	626
regional part of cerebral cortex	3.51e-14	22
embryo	3.65e-14	612
circulatory system	4.63e-14	113
cardiovascular system	8.05e-14	110
embryonic structure	3.49e-13	605
developing anatomical structure	3.49e-13	605
germ layer	3.88e-13	604
embryonic tissue	3.88e-13	604
presumptive structure	3.88e-13	604
epiblast (generic)	3.88e-13	604
neocortex	6.02e-13	20
somite	7.98e-13	83
paraxial mesoderm	7.98e-13	83
presomitic mesoderm	7.98e-13	83
presumptive segmental plate	7.98e-13	83
trunk paraxial mesoderm	7.98e-13	83
presumptive paraxial mesoderm	7.98e-13	83
multilaminar epithelium	1.74e-12	82
systemic artery	4.07e-12	33
systemic arterial system	4.07e-12	33
adult organism	8.90e-12	115
dermomyotome	1.68e-10	70
epithelial tube	3.29e-10	118
skeletal muscle tissue	4.13e-10	61
striated muscle tissue	4.13e-10	61
myotome	4.13e-10	61
posterior neural tube	4.82e-10	15
chordal neural plate	4.82e-10	15
muscle tissue	5.59e-10	63
musculature	5.59e-10	63
musculature of body	5.59e-10	63

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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No analysis results for this cluster

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.