Coexpression cluster:C3136

Full id: C3136_medial_pons_parietal_amygdala_paracentral_brain_frontal

Phase1 CAGE Peaks

Hg19::chr11:26353753..26353767,+	p7@ANO3
Hg19::chr1:236917218..236917230,+	p8@ACTN2
Hg19::chr5:126984919..126984976,+	p3@CTXN3

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:0051370	ZASP binding	0.00256093253267397
GO:0051374	FATZ 1 binding	0.00256093253267397
GO:0051373	FATZ binding	0.00341452645300212
GO:0031143	pseudopodium	0.00512163890781363
GO:0043197	dendritic spine	0.00614578576334893
GO:0030175	filopodium	0.00658447968675831
GO:0051289	protein homotetramerization	0.00658447968675831
GO:0048041	focal adhesion formation	0.00832156070721741
GO:0051262	protein tetramerization	0.00967235568457086
GO:0030035	microspike biogenesis	0.0116364904660761
GO:0005884	actin filament	0.0116364904660761
GO:0005925	focal adhesion	0.0119438065733289
GO:0005924	cell-substrate adherens junction	0.0119438065733289
GO:0030425	dendrite	0.0119438065733289
GO:0030055	cell-matrix junction	0.0119438065733289
GO:0005178	integrin binding	0.0119438065733289
GO:0051260	protein homooligomerization	0.0119438065733289
GO:0008307	structural constituent of muscle	0.0119438065733289
GO:0044463	cell projection part	0.0126612986249979
GO:0030031	cell projection biogenesis	0.0127954278973855
GO:0005912	adherens junction	0.0131602361543361
GO:0051259	protein oligomerization	0.0144213874903024
GO:0043005	neuron projection	0.0180166334790902
GO:0016323	basolateral plasma membrane	0.0181175114842883
GO:0007160	cell-matrix adhesion	0.0195096332609514
GO:0032403	protein complex binding	0.0195096332609514
GO:0031589	cell-substrate adhesion	0.0195096332609514
GO:0032990	cell part morphogenesis	0.0347246198242458
GO:0030030	cell projection organization and biogenesis	0.0347246198242458
GO:0048858	cell projection morphogenesis	0.0347246198242458
GO:0015629	actin cytoskeleton	0.0486932053992805
GO:0042995	cell projection	0.0498681839186583

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
neural tube	2.40e-66	57
neural rod	2.40e-66	57
future spinal cord	2.40e-66	57
neural keel	2.40e-66	57
regional part of brain	1.89e-60	59
central nervous system	8.05e-58	82
regional part of forebrain	2.76e-56	41
forebrain	2.76e-56	41
future forebrain	2.76e-56	41
neural plate	9.14e-55	86
presumptive neural plate	9.14e-55	86
anterior neural tube	1.04e-54	42
brain	2.12e-54	69
future brain	2.12e-54	69
neurectoderm	7.81e-54	90
regional part of nervous system	7.67e-52	94
nervous system	7.67e-52	94
gray matter	1.43e-50	34
brain grey matter	1.43e-50	34
telencephalon	1.81e-50	34
regional part of telencephalon	2.59e-48	33
cerebral hemisphere	4.00e-47	32
adult organism	2.77e-45	115
pre-chordal neural plate	6.75e-41	61
anterior region of body	2.53e-40	129
craniocervical region	2.53e-40	129
regional part of cerebral cortex	7.81e-40	22
head	8.56e-40	123
ectoderm	4.04e-36	173
presumptive ectoderm	4.04e-36	173
ectoderm-derived structure	5.25e-36	169
neocortex	5.90e-36	20
cerebral cortex	1.93e-34	25
pallium	1.93e-34	25
tube	8.07e-18	194
basal ganglion	8.72e-18	9
nuclear complex of neuraxis	8.72e-18	9
aggregate regional part of brain	8.72e-18	9
collection of basal ganglia	8.72e-18	9
cerebral subcortex	8.72e-18	9
nucleus of brain	1.36e-17	9
neural nucleus	1.36e-17	9
gyrus	1.95e-14	6
temporal lobe	9.35e-14	7
anatomical conduit	9.88e-14	241
telencephalic nucleus	9.88e-14	7
brainstem	3.43e-13	8
anatomical cluster	3.88e-13	286
posterior neural tube	9.72e-13	15
chordal neural plate	9.72e-13	15
organ part	4.26e-12	219
organism subdivision	9.79e-12	365
limbic system	1.09e-11	5
epithelium	2.04e-11	309
occipital lobe	3.62e-11	5
cell layer	3.73e-11	312
segmental subdivision of hindbrain	1.64e-10	12
hindbrain	1.64e-10	12
presumptive hindbrain	1.64e-10	12
multi-tissue structure	5.29e-10	347
segmental subdivision of nervous system	1.40e-09	13
organ	2.69e-09	511
embryo	4.31e-09	612
corpus striatum	5.71e-09	4
striatum	5.71e-09	4
ventral part of telencephalon	5.71e-09	4
future corpus striatum	5.71e-09	4
parietal lobe	4.08e-08	5
middle temporal gyrus	5.30e-08	3
germ layer	7.44e-08	604
embryonic tissue	7.44e-08	604
presumptive structure	7.44e-08	604
epiblast (generic)	7.44e-08	604
embryonic structure	8.32e-08	605
developing anatomical structure	8.32e-08	605
pons	9.45e-08	3
medulla oblongata	1.40e-07	3
myelencephalon	1.40e-07	3
future myelencephalon	1.40e-07	3
diencephalon	2.01e-07	7
future diencephalon	2.01e-07	7
brainstem nucleus	3.74e-07	3
caudate-putamen	7.27e-07	3
dorsal striatum	7.27e-07	3
multi-cellular organism	7.69e-07	659

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
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457126365778581

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.