Coexpression cluster:C1373

Full id: C1373_occipital_hippocampus_caudate_amygdala_medial_thalamus_parietal

Phase1 CAGE Peaks

Hg19::chr12:93800048..93800052,-	p@chr12:93800048..93800052 -
Hg19::chr14:90872497..90872510,+	p4@CALM1
Hg19::chr3:178865887..178865938,+	p2@PIK3CA
Hg19::chr7:44259054..44259069,-	p5@CAMK2B
Hg19::chrX:102564877..102564913,-	p@chrX:102564877..102564913 -
Hg19::chrX:13805158..13805159,-	p@chrX:13805158..13805159 -

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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p.value	FDR	nGenes	nPathway	Name
2.74916378593662e-05	0.00193357852944209	2	87	ErbB signaling pathway (KEGG):04012
0.000114222896616409	0.00449698106778368	2	177	Calcium signaling pathway (KEGG):04020
2.20729154564608e-05	0.00193357852944209	2	78	Phosphatidylinositol signaling system (KEGG):04070
4.73033289875392e-05	0.00249525060409269	2	114	Oocyte meiosis (KEGG):04114
1.77542685881244e-05	0.00193357852944209	2	70	Long-term potentiation (KEGG):04720
8.59991458038641e-08	2.7218729646923e-05	3	127	Neurotrophin signaling pathway (KEGG):04722
0.0005478423184049	0.0173392093775151	2	388	Olfactory transduction (KEGG):04740
6.93847325306698e-05	0.00337850274553184	2	138	Insulin signaling pathway (KEGG):04910
3.70989802916306e-05	0.00213487768405474	2	101	GnRH signaling pathway (KEGG):04912
3.70989802916306e-05	0.00213487768405474	2	101	Melanogenesis (KEGG):04916
1.98549864581673e-05	0.00193357852944209	2	74	Gastric acid secretion (KEGG):04971
0.000120772003400194	0.00449698106778368	2	182	Tuberculosis (KEGG):05152
1.12679195761913e-08	7.13259309172909e-06	3	65	Glioma (KEGG):05214
2.74916378593662e-05	0.00193357852944209	2	87	MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544
8.75676438203826e-05	0.00369535456922015	2	155	Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289
0.00136564166399986	0.0360187988879963	1	13	Keap1-Nrf2 Pathway (Wikipathways):WP3
5.73832218607515e-06	0.000908089485946393	2	40	G13 Signaling Pathway (Wikipathways):WP524
8.09096463176418e-05	0.00365827186564766	2	149	Calcium Regulation in the Cardiac Cell (Wikipathways):WP536
0.000948076017669582	0.0272787326902202	2	511	Signaling in Immune system (Reactome):REACT_6900
0.000176480147893589	0.00587957545350747	2	220	Signalling by NGF (Reactome):REACT_11061
0.000789137438324553	0.0237868570694972	2	466	Hemostasis (Reactome):REACT_604
0.000141509562041495	0.00497641959845924	2	197	Synaptic Transmission (Reactome):REACT_13685
0.00115562392354087	0.0318047801565813	1	11	Metabolism of nitric oxide (Reactome):REACT_12508
3.20096624129033e-06	0.00067540387691226	2	30	{CALM1,30} (Static Module):NA

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:0046934	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	0.0111097667590962
GO:0035004	phosphoinositide 3-kinase activity	0.0111097667590962
GO:0016303	1-phosphatidylinositol-3-kinase activity	0.0111097667590962
GO:0005942	phosphoinositide 3-kinase complex	0.0111097667590962
GO:0004683	calmodulin-dependent protein kinase activity	0.0111097667590962
GO:0046854	phosphoinositide phosphorylation	0.0111097667590962
GO:0046834	lipid phosphorylation	0.0111097667590962
GO:0016310	phosphorylation	0.0111097667590962
GO:0016773	phosphotransferase activity, alcohol group as acceptor	0.0111097667590962
GO:0001727	lipid kinase activity	0.0113184485970462
GO:0006793	phosphorus metabolic process	0.0113184485970462
GO:0006796	phosphate metabolic process	0.0113184485970462
GO:0016301	kinase activity	0.0113184485970462
GO:0030258	lipid modification	0.0128916966733399
GO:0016772	transferase activity, transferring phosphorus-containing groups	0.0130998092213604
GO:0004428	inositol or phosphatidylinositol kinase activity	0.0143142684290914
GO:0030384	phosphoinositide metabolic process	0.0163266350470889
GO:0006650	glycerophospholipid metabolic process	0.0194612206254854
GO:0043412	biopolymer modification	0.0213143187492112
GO:0048015	phosphoinositide-mediated signaling	0.0223615365053458
GO:0005516	calmodulin binding	0.0232736708268528
GO:0016740	transferase activity	0.0247950620212862
GO:0044445	cytosolic part	0.0286138871299826
GO:0006644	phospholipid metabolic process	0.0310183030141691
GO:0019932	second-messenger-mediated signaling	0.0361926776864339
GO:0006643	membrane lipid metabolic process	0.0361926776864339

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	1.10e-36	56
neural rod	1.10e-36	56
future spinal cord	1.10e-36	56
neural keel	1.10e-36	56
adult organism	1.35e-36	114
regional part of nervous system	1.62e-34	53
regional part of brain	1.62e-34	53
central nervous system	8.45e-32	81
nervous system	9.30e-32	89
regional part of forebrain	5.67e-31	41
forebrain	5.67e-31	41
anterior neural tube	5.67e-31	41
future forebrain	5.67e-31	41
brain	2.73e-27	68
future brain	2.73e-27	68
neurectoderm	1.41e-26	86
neural plate	2.89e-26	82
presumptive neural plate	2.89e-26	82
brain grey matter	3.06e-26	34
gray matter	3.06e-26	34
telencephalon	4.62e-26	34
cerebral hemisphere	7.23e-25	32
regional part of telencephalon	8.92e-25	32
structure with developmental contribution from neural crest	9.50e-22	132
ecto-epithelium	1.24e-21	104
ectoderm-derived structure	1.39e-20	171
ectoderm	1.39e-20	171
presumptive ectoderm	1.39e-20	171
pre-chordal neural plate	7.20e-20	61
cerebral cortex	8.69e-20	25
pallium	8.69e-20	25
regional part of cerebral cortex	1.36e-18	22
neocortex	5.02e-17	20
organ system subdivision	1.64e-13	223
basal ganglion	5.51e-08	9
nuclear complex of neuraxis	5.51e-08	9
aggregate regional part of brain	5.51e-08	9
collection of basal ganglia	5.51e-08	9
cerebral subcortex	5.51e-08	9
neural nucleus	7.07e-08	9
nucleus of brain	7.07e-08	9
posterior neural tube	2.98e-07	15
chordal neural plate	2.98e-07	15
tube	5.62e-07	192

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.