Coexpression cluster:C4536

Full id: C4536_occipital_brain_medial_frontal_parietal_insula_postcentral

Phase1 CAGE Peaks

Hg19::chr6:101847105..101847116,+	p13@GRIK2
Hg19::chr6:99797658..99797684,-	p6@C6orf168
Hg19::chr7:39018373..39018384,+	p@chr7:39018373..39018384 +

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:0048172	regulation of short-term neuronal synaptic plasticity	0.00114800423878488
GO:0031557	induction of programmed cell death in response to chemical stimulus	0.00114800423878488
GO:0050806	positive regulation of synaptic transmission	0.00295201089973255
GO:0051971	positive regulation of transmission of nerve impulse	0.00295201089973255
GO:0015277	kainate selective glutamate receptor activity	0.00295201089973255
GO:0031646	positive regulation of neurological process	0.00295201089973255
GO:0048168	regulation of neuronal synaptic plasticity	0.00295201089973255
GO:0050804	regulation of synaptic transmission	0.00375710478147779
GO:0048167	regulation of synaptic plasticity	0.00375710478147779
GO:0050803	regulation of synapse structure and activity	0.00375710478147779
GO:0051969	regulation of transmission of nerve impulse	0.00375710478147779
GO:0007215	glutamate signaling pathway	0.00401801483574708
GO:0031644	regulation of neurological process	0.00441540091840339
GO:0051402	neuron apoptosis	0.00492001816622092
GO:0004970	ionotropic glutamate receptor activity	0.0055965206640763
GO:0005234	extracellular-glutamate-gated ion channel activity	0.0055965206640763
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.00972427119911899
GO:0008066	glutamate receptor activity	0.0119902664939754
GO:0005230	extracellular ligand-gated ion channel activity	0.0158303742400863
GO:0045211	postsynaptic membrane	0.0163715387096279
GO:0044456	synapse part	0.0163715387096279
GO:0015276	ligand-gated ion channel activity	0.0163715387096279
GO:0022834	ligand-gated channel activity	0.0163715387096279
GO:0012502	induction of programmed cell death	0.0203770752384317
GO:0043068	positive regulation of programmed cell death	0.0236948074885199
GO:0051239	regulation of multicellular organismal process	0.0244613210879548
GO:0007268	synaptic transmission	0.0246608317961197
GO:0019226	transmission of nerve impulse	0.027060099914215
GO:0030054	cell junction	0.0339650909268079
GO:0022836	gated channel activity	0.038649476039091
GO:0043067	regulation of programmed cell death	0.0422609060402684
GO:0042221	response to chemical stimulus	0.0422609060402684
GO:0007267	cell-cell signaling	0.0433138896579377
GO:0005216	ion channel activity	0.0433138896579377
GO:0022838	substrate specific channel activity	0.0433138896579377
GO:0022803	passive transmembrane transporter activity	0.0433138896579377
GO:0015267	channel activity	0.0433138896579377

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
central nervous system	5.58e-29	82
regional part of nervous system	2.89e-28	94
nervous system	2.89e-28	94
neural tube	1.67e-27	57
neural rod	1.67e-27	57
future spinal cord	1.67e-27	57
neural keel	1.67e-27	57
brain	2.25e-27	69
future brain	2.25e-27	69
head	8.49e-27	123
neural plate	2.10e-26	86
presumptive neural plate	2.10e-26	86
neurectoderm	3.51e-26	90
anterior region of body	2.17e-25	129
craniocervical region	2.17e-25	129
ectoderm	2.36e-25	173
presumptive ectoderm	2.36e-25	173
ectoderm-derived structure	3.33e-25	169
regional part of brain	1.05e-24	59
cerebral hemisphere	6.01e-22	32
telencephalon	1.14e-21	34
regional part of forebrain	1.20e-21	41
forebrain	1.20e-21	41
future forebrain	1.20e-21	41
gray matter	2.34e-21	34
brain grey matter	2.34e-21	34
anterior neural tube	8.68e-21	42
regional part of telencephalon	9.68e-21	33
pre-chordal neural plate	2.58e-20	61
cerebral cortex	2.77e-18	25
pallium	2.77e-18	25
neocortex	5.37e-17	20
regional part of cerebral cortex	1.15e-16	22
organism subdivision	2.22e-14	365
adult organism	9.99e-14	115
organ part	9.90e-13	219
multi-tissue structure	2.39e-09	347
cell layer	9.59e-09	312
epithelium	4.04e-08	309
anatomical cluster	4.27e-08	286
posterior neural tube	7.25e-08	15
chordal neural plate	7.25e-08	15
organ	1.92e-07	511
gyrus	2.82e-07	6

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)
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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.