Coexpression cluster:C2230

Full id: C2230_pons_cerebellum_merkel_occipital_paracentral_medulla_postcentral

Phase1 CAGE Peaks

Hg19::chr12:65218487..65218501,+	p7@TBC1D30
Hg19::chr21:31312141..31312150,-	p9@GRIK1
Hg19::chr3:56809691..56809715,-	p12@ARHGEF3
Hg19::chr9:135457981..135458003,+	p1@BARHL1

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:0051966	regulation of synaptic transmission, glutamatergic	0.0211920527965079
GO:0035249	synaptic transmission, glutamatergic	0.0211920527965079
GO:0015277	kainate selective glutamate receptor activity	0.0278006519143408
GO:0007399	nervous system development	0.0278006519143408
GO:0050804	regulation of synaptic transmission	0.0278006519143408
GO:0051969	regulation of transmission of nerve impulse	0.0278006519143408
GO:0007270	nerve-nerve synaptic transmission	0.0278006519143408
GO:0007215	glutamate signaling pathway	0.0278006519143408
GO:0031644	regulation of neurological process	0.0294152147210372
GO:0001764	neuron migration	0.0344016163843688
GO:0004970	ionotropic glutamate receptor activity	0.0344016163843688
GO:0005234	extracellular-glutamate-gated ion channel activity	0.0344016163843688
GO:0050877	neurological system process	0.0376508935600235
GO:0050789	regulation of biological process	0.0457532010981795
GO:0003008	system process	0.0457532010981795
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0457532010981795
GO:0048731	system development	0.0457532010981795

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	2.87e-71	57
neural rod	2.87e-71	57
future spinal cord	2.87e-71	57
neural keel	2.87e-71	57
central nervous system	1.85e-63	82
regional part of nervous system	4.13e-63	94
nervous system	4.13e-63	94
regional part of brain	1.06e-61	59
brain	8.34e-56	69
future brain	8.34e-56	69
neural plate	1.11e-52	86
presumptive neural plate	1.11e-52	86
regional part of forebrain	5.78e-50	41
forebrain	5.78e-50	41
future forebrain	5.78e-50	41
neurectoderm	9.04e-50	90
anterior neural tube	1.39e-48	42
gray matter	2.71e-46	34
brain grey matter	2.71e-46	34
telencephalon	3.59e-46	34
cerebral hemisphere	7.58e-46	32
regional part of cerebral cortex	1.06e-44	22
regional part of telencephalon	8.54e-44	33
neocortex	2.66e-40	20
cerebral cortex	8.39e-39	25
pallium	8.39e-39	25
adult organism	3.40e-38	115
pre-chordal neural plate	2.50e-35	61
ectoderm-derived structure	5.23e-32	169
ectoderm	6.15e-31	173
presumptive ectoderm	6.15e-31	173
head	2.00e-29	123
anterior region of body	6.87e-29	129
craniocervical region	6.87e-29	129
posterior neural tube	4.20e-23	15
chordal neural plate	4.20e-23	15
segmental subdivision of hindbrain	9.47e-21	12
hindbrain	9.47e-21	12
presumptive hindbrain	9.47e-21	12
segmental subdivision of nervous system	5.77e-19	13
tube	3.06e-17	194
gyrus	1.00e-15	6
regional part of metencephalon	6.81e-14	9
metencephalon	6.81e-14	9
future metencephalon	6.81e-14	9
parietal lobe	2.15e-13	5
occipital lobe	5.17e-13	5
organ part	5.46e-12	219
brainstem	8.96e-12	8
epithelium	9.29e-12	309
anatomical cluster	1.63e-11	286
cell layer	1.64e-11	312
anatomical conduit	1.73e-11	241
temporal lobe	8.37e-11	7
nucleus of brain	3.02e-09	9
neural nucleus	3.02e-09	9
organism subdivision	6.89e-09	365
medulla oblongata	7.30e-09	3
myelencephalon	7.30e-09	3
future myelencephalon	7.30e-09	3
pons	7.89e-09	3
limbic system	2.77e-08	5
middle temporal gyrus	3.07e-08	3
cerebellum	2.30e-07	6
rhombic lip	2.30e-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.