Coexpression cluster:C2685

Full id: C2685_occipital_medial_parietal_hippocampus_amygdala_caudate_temporal

Phase1 CAGE Peaks

Hg19::chr2:210489781..210489790,+	p57@MAP2
Hg19::chr3:35786039..35786054,+	p1@MIR128-2
Hg19::chr5:175308859..175308869,+	p39@CPLX2
Hg19::chrX:18622158..18622169,+	p3@CDKL5

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:0043303	mast cell degranulation	0.016686285279565
GO:0002448	mast cell mediated immunity	0.016686285279565
GO:0045576	mast cell activation	0.016686285279565
GO:0043299	leukocyte degranulation	0.016686285279565
GO:0002444	myeloid leukocyte mediated immunity	0.016686285279565
GO:0019905	syntaxin binding	0.01919116716192
GO:0000149	SNARE binding	0.01919116716192
GO:0007026	negative regulation of microtubule depolymerization	0.01919116716192
GO:0031114	regulation of microtubule depolymerization	0.01919116716192
GO:0007019	microtubule depolymerization	0.01919116716192
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.01919116716192
GO:0002274	myeloid leukocyte activation	0.01919116716192
GO:0031110	regulation of microtubule polymerization or depolymerization	0.01919116716192
GO:0004693	cyclin-dependent protein kinase activity	0.01919116716192
GO:0031109	microtubule polymerization or depolymerization	0.0195536312730498
GO:0006904	vesicle docking during exocytosis	0.0195536312730498
GO:0048278	vesicle docking	0.0195536312730498
GO:0022406	membrane docking	0.0195536312730498
GO:0046777	protein amino acid autophosphorylation	0.0202839508929141
GO:0051261	protein depolymerization	0.0202839508929141
GO:0016540	protein autoprocessing	0.0202839508929141
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0213340109531962
GO:0045055	regulated secretory pathway	0.0213340109531962
GO:0006836	neurotransmitter transport	0.0288641825117031
GO:0002443	leukocyte mediated immunity	0.0288641825117031
GO:0016485	protein processing	0.0330935746589501
GO:0051128	regulation of cellular component organization and biogenesis	0.0330935746589501
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0330935746589501
GO:0051248	negative regulation of protein metabolic process	0.0330935746589501
GO:0002252	immune effector process	0.0330935746589501
GO:0006887	exocytosis	0.0330935746589501
GO:0005516	calmodulin binding	0.0406881110191871
GO:0045321	leukocyte activation	0.0488306617395578
GO:0005875	microtubule associated complex	0.0488306617395578

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
telencephalon	4.68e-77	34
brain grey matter	7.62e-77	34
gray matter	7.62e-77	34
cerebral hemisphere	2.86e-76	32
regional part of telencephalon	6.22e-76	32
regional part of forebrain	4.71e-73	41
forebrain	4.71e-73	41
anterior neural tube	4.71e-73	41
future forebrain	4.71e-73	41
regional part of cerebral cortex	3.03e-72	22
neural tube	5.03e-72	56
neural rod	5.03e-72	56
future spinal cord	5.03e-72	56
neural keel	5.03e-72	56
regional part of nervous system	7.30e-72	53
regional part of brain	7.30e-72	53
neocortex	1.33e-64	20
central nervous system	2.55e-63	81
cerebral cortex	2.85e-63	25
pallium	2.85e-63	25
nervous system	2.68e-59	89
brain	3.75e-57	68
future brain	3.75e-57	68
pre-chordal neural plate	4.34e-47	61
neural plate	7.66e-47	82
presumptive neural plate	7.66e-47	82
neurectoderm	2.64e-44	86
ecto-epithelium	1.16e-37	104
adult organism	1.45e-33	114
structure with developmental contribution from neural crest	7.78e-32	132
ectoderm-derived structure	2.31e-30	171
ectoderm	2.31e-30	171
presumptive ectoderm	2.31e-30	171
organ system subdivision	4.62e-28	223
gyrus	1.12e-23	6
basal ganglion	9.32e-21	9
nuclear complex of neuraxis	9.32e-21	9
aggregate regional part of brain	9.32e-21	9
collection of basal ganglia	9.32e-21	9
cerebral subcortex	9.32e-21	9
occipital lobe	2.02e-20	5
tube	2.34e-20	192
temporal lobe	2.65e-20	6
limbic system	5.20e-20	5
corpus striatum	1.63e-16	4
striatum	1.63e-16	4
ventral part of telencephalon	1.63e-16	4
future corpus striatum	1.63e-16	4
anatomical conduit	1.34e-15	240
neural nucleus	3.71e-15	9
nucleus of brain	3.71e-15	9
organ part	1.24e-14	218
telencephalic nucleus	5.39e-14	7
anatomical cluster	9.78e-14	373
caudate-putamen	4.56e-13	3
dorsal striatum	4.56e-13	3
parietal lobe	5.22e-13	5
frontal cortex	7.07e-13	3
epithelium	3.89e-11	306
cell layer	6.10e-11	309
multi-tissue structure	1.49e-10	342
Ammon's horn	2.81e-09	2
lobe parts of cerebral cortex	2.81e-09	2
hippocampal formation	2.81e-09	2
limbic lobe	2.81e-09	2
caudate nucleus	2.92e-09	2
future caudate nucleus	2.92e-09	2
middle frontal gyrus	3.57e-09	2
middle temporal gyrus	3.87e-09	2
amygdala	5.31e-09	2
germ layer	6.74e-07	560
germ layer / neural crest	6.74e-07	560
embryonic tissue	6.74e-07	560
presumptive structure	6.74e-07	560
germ layer / neural crest derived structure	6.74e-07	560
epiblast (generic)	6.74e-07	560
embryonic structure	8.98e-07	564

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.