Coexpression cluster:C2359

Full id: C2359_cord_cerebellum_occipital_frontal_parietal_postcentral_brain

Phase1 CAGE Peaks

Hg19::chr16:10276731..10276772,-	p1@GRIN2A
Hg19::chr16:10277298..10277308,-	p@chr16:10277298..10277308 -
Hg19::chr1:66820232..66820259,+	p22@PDE4B
Hg19::chr7:151511577..151511596,-	p25@PRKAG2

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:0016595	glutamate binding	0.0144622987337513
GO:0008328	ionotropic glutamate receptor complex	0.0144622987337513
GO:0017146	N-methyl-D-aspartate selective glutamate receptor complex	0.0144622987337513
GO:0004972	N-methyl-D-aspartate selective glutamate receptor activity	0.0144622987337513
GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.0144622987337513
GO:0007613	memory	0.0177063306952289
GO:0042734	presynaptic membrane	0.0177063306952289
GO:0048167	regulation of synaptic plasticity	0.0180704237443215
GO:0050803	regulation of synapse structure and activity	0.0180704237443215
GO:0016597	amino acid binding	0.0180704237443215
GO:0005626	insoluble fraction	0.0180704237443215
GO:0007215	glutamate signaling pathway	0.0180704237443215
GO:0006695	cholesterol biosynthetic process	0.0198552699367001
GO:0016126	sterol biosynthetic process	0.0225114542956761
GO:0004970	ionotropic glutamate receptor activity	0.0225114542956761
GO:0005234	extracellular-glutamate-gated ion channel activity	0.0225114542956761
GO:0007611	learning and/or memory	0.0225114542956761
GO:0043176	amine binding	0.0225114542956761
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0225114542956761
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0225114542956761
GO:0005977	glycogen metabolic process	0.0225114542956761
GO:0006073	glucan metabolic process	0.0225114542956761
GO:0006112	energy reserve metabolic process	0.0246677940691695
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0284869167389958
GO:0006633	fatty acid biosynthetic process	0.0284869167389958
GO:0008203	cholesterol metabolic process	0.0284869167389958
GO:0043005	neuron projection	0.0284869167389958
GO:0016053	organic acid biosynthetic process	0.0284869167389958
GO:0046394	carboxylic acid biosynthetic process	0.0284869167389958
GO:0044264	cellular polysaccharide metabolic process	0.0284869167389958
GO:0005976	polysaccharide metabolic process	0.0284869167389958
GO:0006694	steroid biosynthetic process	0.0284869167389958
GO:0016125	sterol metabolic process	0.0284869167389958
GO:0008066	glutamate receptor activity	0.0284869167389958
GO:0043235	receptor complex	0.0323680396493635
GO:0015980	energy derivation by oxidation of organic compounds	0.033464591504368
GO:0005230	extracellular ligand-gated ion channel activity	0.0364411892024579
GO:0008081	phosphoric diester hydrolase activity	0.0373704950705004
GO:0045211	postsynaptic membrane	0.039301958964788
GO:0044456	synapse part	0.0401508769760526
GO:0015276	ligand-gated ion channel activity	0.0401508769760526
GO:0022834	ligand-gated channel activity	0.0401508769760526
GO:0006631	fatty acid metabolic process	0.0456372653621256

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	2.45e-77	56
neural rod	2.45e-77	56
future spinal cord	2.45e-77	56
neural keel	2.45e-77	56
regional part of nervous system	3.82e-71	53
regional part of brain	3.82e-71	53
central nervous system	2.17e-65	81
brain	4.40e-61	68
future brain	4.40e-61	68
nervous system	3.55e-60	89
telencephalon	1.33e-55	34
brain grey matter	1.50e-55	34
gray matter	1.50e-55	34
regional part of forebrain	2.71e-55	41
forebrain	2.71e-55	41
anterior neural tube	2.71e-55	41
future forebrain	2.71e-55	41
cerebral hemisphere	1.19e-51	32
neural plate	1.48e-51	82
presumptive neural plate	1.48e-51	82
regional part of telencephalon	4.19e-51	32
neurectoderm	1.38e-48	86
regional part of cerebral cortex	2.56e-46	22
adult organism	2.41e-45	114
neocortex	9.63e-42	20
cerebral cortex	3.16e-40	25
pallium	3.16e-40	25
ecto-epithelium	5.43e-40	104
pre-chordal neural plate	1.05e-36	61
structure with developmental contribution from neural crest	6.50e-32	132
ectoderm-derived structure	2.36e-30	171
ectoderm	2.36e-30	171
presumptive ectoderm	2.36e-30	171
organ system subdivision	3.36e-25	223
posterior neural tube	3.87e-22	15
chordal neural plate	3.87e-22	15
tube	7.96e-18	192
basal ganglion	1.33e-16	9
nuclear complex of neuraxis	1.33e-16	9
aggregate regional part of brain	1.33e-16	9
collection of basal ganglia	1.33e-16	9
cerebral subcortex	1.33e-16	9
neural nucleus	1.76e-16	9
nucleus of brain	1.76e-16	9
segmental subdivision of hindbrain	2.37e-16	12
hindbrain	2.37e-16	12
presumptive hindbrain	2.37e-16	12
gyrus	4.74e-16	6
brainstem	5.17e-15	6
segmental subdivision of nervous system	6.11e-15	13
anatomical conduit	2.81e-13	240
temporal lobe	3.35e-13	6
occipital lobe	3.37e-13	5
limbic system	4.12e-13	5
anatomical cluster	4.44e-13	373
telencephalic nucleus	3.60e-12	7
regional part of metencephalon	2.64e-10	9
metencephalon	2.64e-10	9
future metencephalon	2.64e-10	9
parietal lobe	4.66e-09	5
frontal cortex	4.71e-09	3
pons	2.03e-08	3
epithelium	2.06e-08	306
medulla oblongata	2.82e-08	3
myelencephalon	2.82e-08	3
future myelencephalon	2.82e-08	3
multi-tissue structure	2.82e-08	342
organ part	3.09e-08	218
cell layer	3.24e-08	309
spinal cord	1.15e-07	3
dorsal region element	1.15e-07	3
dorsum	1.15e-07	3

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.