Coexpression cluster:C1395

Full id: C1395_temporal_occipital_duodenum_parietal_medial_cerebellum_brain

Phase1 CAGE Peaks

Hg19::chr14:60074147..60074162,-	p12@RTN1
Hg19::chr16:56390504..56390515,+	p@chr16:56390504..56390515 +
Hg19::chr17:30814707..30814718,+	p17@CDK5R1
Hg19::chr19:42471082..42471122,-	p@chr19:42471082..42471122 -
Hg19::chr6:109761966..109761979,-	p4@PPIL6
Hg19::chrX:99665097..99665125,-	p2@PCDH19

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:0030182	neuron differentiation	0.00720561611857918
GO:0016533	cyclin-dependent protein kinase 5 activator complex	0.00720561611857918
GO:0043539	protein serine/threonine kinase activator activity	0.00720561611857918
GO:0035235	ionotropic glutamate receptor signaling pathway	0.00720561611857918
GO:0016534	cyclin-dependent protein kinase 5 activator activity	0.00720561611857918
GO:0048699	generation of neurons	0.00765940106601726
GO:0022008	neurogenesis	0.00769157031996023
GO:0007413	axonal fasciculation	0.00969772650622996
GO:0016337	cell-cell adhesion	0.00969772650622996
GO:0031594	neuromuscular junction	0.00969772650622996
GO:0043197	dendritic spine	0.00969772650622996
GO:0007213	acetylcholine receptor signaling, muscarinic pathway	0.00969772650622996
GO:0007158	neuron adhesion	0.00969772650622996
GO:0043525	positive regulation of neuron apoptosis	0.011576875510383
GO:0008038	neuron recognition	0.01320504727344
GO:0030295	protein kinase activator activity	0.013504565630361
GO:0045296	cadherin binding	0.0137687530116964
GO:0050839	cell adhesion molecule binding	0.0140034979185793
GO:0030426	growth cone	0.0162011855987303
GO:0019209	kinase activator activity	0.0162011855987303
GO:0030427	site of polarized growth	0.0162861869441539
GO:0007215	glutamate signaling pathway	0.0171807993626783
GO:0007399	nervous system development	0.0172130658216937
GO:0043523	regulation of neuron apoptosis	0.0187147571999021
GO:0045664	regulation of neuron differentiation	0.0187147571999021
GO:0051402	neuron apoptosis	0.0207597465600854
GO:0030424	axon	0.0213659970292782
GO:0043025	cell soma	0.0213659970292782
GO:0001764	neuron migration	0.0213659970292782
GO:0008037	cell recognition	0.0213659970292782
GO:0030425	dendrite	0.0213659970292782
GO:0022610	biological adhesion	0.0213659970292782
GO:0007155	cell adhesion	0.0213659970292782
GO:0044463	cell projection part	0.0248523245329768
GO:0000079	regulation of cyclin-dependent protein kinase activity	0.0251673650516551
GO:0030176	integral to endoplasmic reticulum membrane	0.0264610062785568
GO:0007411	axon guidance	0.0271995516014897
GO:0031227	intrinsic to endoplasmic reticulum membrane	0.028842026336961
GO:0043292	contractile fiber	0.0291797408887818
GO:0048468	cell development	0.0291797408887818
GO:0043005	neuron projection	0.0354647600560195
GO:0005509	calcium ion binding	0.0379224089843669
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	0.0379224089843669
GO:0016859	cis-trans isomerase activity	0.0379224089843669
GO:0019887	protein kinase regulator activity	0.041766460181213
GO:0048731	system development	0.041766460181213
GO:0007409	axonogenesis	0.0434780166963583
GO:0048667	neuron morphogenesis during differentiation	0.0437219029656972
GO:0048812	neurite morphogenesis	0.0437219029656972
GO:0019207	kinase regulator activity	0.0437219029656972
GO:0000904	cellular morphogenesis during differentiation	0.0442621846464368
GO:0031175	neurite development	0.0444436574628336
GO:0048869	cellular developmental process	0.0444436574628336
GO:0030154	cell differentiation	0.0444436574628336
GO:0007420	brain development	0.0444436574628336
GO:0031301	integral to organelle membrane	0.0444436574628336
GO:0045595	regulation of cell differentiation	0.0452245969787288
GO:0031300	intrinsic to organelle membrane	0.0467050532889091
GO:0048666	neuron development	0.0467050532889091
GO:0048856	anatomical structure development	0.0491735817345141

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	2.35e-88	56
neural rod	2.35e-88	56
future spinal cord	2.35e-88	56
neural keel	2.35e-88	56
central nervous system	5.03e-87	81
regional part of nervous system	7.63e-85	53
regional part of brain	7.63e-85	53
nervous system	1.98e-80	89
brain grey matter	7.39e-77	34
gray matter	7.39e-77	34
telencephalon	1.13e-76	34
regional part of forebrain	4.09e-76	41
forebrain	4.09e-76	41
anterior neural tube	4.09e-76	41
future forebrain	4.09e-76	41
brain	1.09e-73	68
future brain	1.09e-73	68
cerebral hemisphere	1.07e-71	32
regional part of telencephalon	1.92e-71	32
neural plate	9.65e-63	82
presumptive neural plate	9.65e-63	82
regional part of cerebral cortex	3.04e-61	22
neurectoderm	2.61e-59	86
cerebral cortex	4.06e-58	25
pallium	4.06e-58	25
neocortex	1.90e-55	20
pre-chordal neural plate	1.85e-54	61
ecto-epithelium	2.19e-49	104
adult organism	3.80e-42	114
ectoderm-derived structure	2.62e-41	171
ectoderm	2.62e-41	171
presumptive ectoderm	2.62e-41	171
structure with developmental contribution from neural crest	2.42e-40	132
organ system subdivision	5.61e-33	223
tube	1.24e-22	192
basal ganglion	3.94e-20	9
nuclear complex of neuraxis	3.94e-20	9
aggregate regional part of brain	3.94e-20	9
collection of basal ganglia	3.94e-20	9
cerebral subcortex	3.94e-20	9
neural nucleus	1.18e-19	9
nucleus of brain	1.18e-19	9
gyrus	1.32e-18	6
anatomical cluster	1.19e-17	373
temporal lobe	3.59e-16	6
occipital lobe	8.09e-16	5
anatomical conduit	8.79e-16	240
limbic system	9.41e-16	5
parietal lobe	1.06e-15	5
telencephalic nucleus	1.61e-14	7
posterior neural tube	3.66e-14	15
chordal neural plate	3.66e-14	15
organ part	1.97e-13	218
epithelium	4.69e-12	306
cell layer	7.99e-12	309
brainstem	8.43e-12	6
segmental subdivision of hindbrain	5.57e-11	12
hindbrain	5.57e-11	12
presumptive hindbrain	5.57e-11	12
frontal cortex	3.30e-10	3
segmental subdivision of nervous system	4.69e-10	13
multi-tissue structure	1.28e-09	342
pons	2.10e-09	3
germ layer	4.10e-08	560
germ layer / neural crest	4.10e-08	560
embryonic tissue	4.10e-08	560
presumptive structure	4.10e-08	560
germ layer / neural crest derived structure	4.10e-08	560
epiblast (generic)	4.10e-08	560
regional part of metencephalon	4.78e-08	9
metencephalon	4.78e-08	9
future metencephalon	4.78e-08	9
embryo	4.98e-08	592
embryonic structure	5.93e-08	564
middle frontal gyrus	1.62e-07	2
amygdala	1.72e-07	2
middle temporal gyrus	1.89e-07	2
corpus striatum	2.26e-07	4
striatum	2.26e-07	4
ventral part of telencephalon	2.26e-07	4
future corpus striatum	2.26e-07	4
Ammon's horn	2.28e-07	2
lobe parts of cerebral cortex	2.28e-07	2
hippocampal formation	2.28e-07	2
limbic lobe	2.28e-07	2
developing anatomical structure	2.70e-07	581
dorsal plus ventral thalamus	5.33e-07	2
thalamic complex	5.33e-07	2
organ	6.04e-07	503
locus ceruleus	6.38e-07	2
brainstem nucleus	6.38e-07	2
hindbrain nucleus	6.38e-07	2

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.