Coexpression cluster:C4292

Full id: C4292_synovial_Pericytes_Astrocyte_Ciliary_Lens_Smooth_Fibroblast

Phase1 CAGE Peaks

Hg19::chr3:147123837..147123848,-	p7@ZIC4
Hg19::chr3:147127358..147127369,+	p16@ZIC1
Hg19::chr3:147127489..147127503,+	p11@ZIC1

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:0008589	regulation of smoothened signaling pathway	0.0197690591558547
GO:0007224	smoothened signaling pathway	0.0197690591558547
GO:0042472	inner ear morphogenesis	0.0197690591558547
GO:0042471	ear morphogenesis	0.0197690591558547
GO:0048839	inner ear development	0.0197690591558547
GO:0043583	ear development	0.0197690591558547
GO:0007423	sensory organ development	0.0328060999854834
GO:0048598	embryonic morphogenesis	0.0328060999854834
GO:0007389	pattern specification process	0.0388635391999214
GO:0007420	brain development	0.0391996244308409
GO:0003677	DNA binding	0.0464642615688377

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
glial cell (sensu Vertebrata)	7.75e-16	15
glial cell	7.75e-16	15
glioblast	7.75e-16	15
glioblast (sensu Vertebrata)	7.75e-16	15
neuron associated cell	8.34e-14	17
neuron associated cell (sensu Vertebrata)	8.34e-14	17
oligodendrocyte	2.27e-13	7
macroglial cell	2.27e-13	7
astrocyte	2.27e-13	7
oligodendrocyte precursor cell	2.27e-13	7
neural cell	5.81e-12	25
neurectodermal cell	1.63e-11	59
migratory neural crest cell	7.48e-11	41
ectodermal cell	1.44e-08	71
astrocyte of the cerebellum	1.77e-07	3
ciliated cell	1.92e-07	3
multi-ciliated epithelial cell	1.92e-07	3
ciliated epithelial cell	1.92e-07	3
non-pigmented ciliary epithelial cell	1.92e-07	3
leptomeningeal cell	3.12e-07	3

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	3.07e-52	94
nervous system	3.07e-52	94
central nervous system	1.02e-51	82
brain	6.24e-49	69
future brain	6.24e-49	69
regional part of brain	1.72e-45	59
neural plate	7.21e-42	86
presumptive neural plate	7.21e-42	86
neural tube	7.65e-42	57
neural rod	7.65e-42	57
future spinal cord	7.65e-42	57
neural keel	7.65e-42	57
neurectoderm	3.22e-41	90
head	3.42e-34	123
ectoderm	3.17e-32	173
presumptive ectoderm	3.17e-32	173
ectoderm-derived structure	3.89e-32	169
anterior region of body	7.67e-32	129
craniocervical region	7.67e-32	129
pre-chordal neural plate	1.15e-25	61
regional part of forebrain	1.15e-24	41
forebrain	1.15e-24	41
future forebrain	1.15e-24	41
telencephalon	4.05e-24	34
anterior neural tube	6.69e-24	42
regional part of telencephalon	6.93e-23	33
gray matter	3.61e-22	34
brain grey matter	3.61e-22	34
cerebral hemisphere	1.28e-21	32
posterior neural tube	1.67e-20	15
chordal neural plate	1.67e-20	15
segmental subdivision of hindbrain	6.84e-19	12
hindbrain	6.84e-19	12
presumptive hindbrain	6.84e-19	12
segmental subdivision of nervous system	3.33e-17	13
cerebral cortex	7.71e-15	25
pallium	7.71e-15	25
regional part of metencephalon	4.47e-14	9
metencephalon	4.47e-14	9
future metencephalon	4.47e-14	9
cerebellum	7.76e-13	6
rhombic lip	7.76e-13	6
organism subdivision	3.39e-12	365
vasculature of head	1.49e-11	11
vasculature of organ	1.49e-11	11
adult organism	1.82e-11	115
regional part of cerebral cortex	4.94e-11	22
atypical epithelium	4.30e-09	4
nucleus of brain	4.87e-09	9
neural nucleus	4.87e-09	9
basal ganglion	5.20e-09	9
nuclear complex of neuraxis	5.20e-09	9
aggregate regional part of brain	5.20e-09	9
collection of basal ganglia	5.20e-09	9
cerebral subcortex	5.20e-09	9
neocortex	7.87e-09	20
telencephalic nucleus	1.10e-08	7
cell layer	1.45e-08	312
brainstem	5.19e-08	8
organ part	1.64e-07	219
ciliary epithelium	1.92e-07	3
ciliary body	1.92e-07	3
brain vasculature	2.63e-07	5
blood-cerebrospinal fluid barrier	3.12e-07	3
epithelium	3.66e-07	309
articulation	8.56e-07	5
skeletal joint	8.56e-07	5
articular system	8.56e-07	5

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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259647837921719
SUZ12#23512	2	33.4105206073753	0.0011782676453603	0.00800163174548306

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.