Coexpression cluster:C1126

Full id: C1126_thalamus_cerebellum_amygdala_locus_pons_spinal_medulla

Phase1 CAGE Peaks

Hg19::chr11:105481109..105481122,+	p12@GRIA4
Hg19::chr14:24540154..24540163,+	p4@CPNE6
Hg19::chr17:7556584..7556598,+	p@chr17:7556584..7556598 +
Hg19::chr19:1446310..1446318,+	p5@APC2
Hg19::chr3:133508752..133508754,+	p@chr3:133508752..133508754 +
Hg19::chr4:62067884..62067900,+	p6@LPHN3
Hg19::chr6:154360705..154360715,+	p6@OPRM1

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:0007154	cell communication	0.00588720122453785
GO:0007166	cell surface receptor linked signal transduction	0.00588720122453785
GO:0016342	catenin complex	0.00588720122453785
GO:0004988	mu-opioid receptor activity	0.0132446430939913
GO:0005886	plasma membrane	0.0147145373515791
GO:0001786	phosphatidylserine binding	0.0147145373515791
GO:0008013	beta-catenin binding	0.0226970832208509
GO:0004888	transmembrane receptor activity	0.0274525859783805
GO:0004985	opioid receptor activity	0.0274525859783805
GO:0007165	signal transduction	0.0276534821809206
GO:0044459	plasma membrane part	0.0299039553205555
GO:0007215	glutamate signaling pathway	0.0308714336123091
GO:0016524	latrotoxin receptor activity	0.0312070052652059
GO:0030424	axon	0.040427248833855
GO:0004970	ionotropic glutamate receptor activity	0.040427248833855
GO:0030425	dendrite	0.040427248833855
GO:0005234	extracellular-glutamate-gated ion channel activity	0.040427248833855
GO:0004872	receptor activity	0.0434583751946277
GO:0008017	microtubule binding	0.0440268129608783
GO:0019897	extrinsic to plasma membrane	0.0440268129608783

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	4.73e-70	82
regional part of nervous system	6.39e-68	94
nervous system	6.39e-68	94
neural tube	9.07e-68	57
neural rod	9.07e-68	57
future spinal cord	9.07e-68	57
neural keel	9.07e-68	57
brain	6.29e-60	69
future brain	6.29e-60	69
regional part of brain	2.27e-56	59
regional part of forebrain	1.27e-54	41
forebrain	1.27e-54	41
future forebrain	1.27e-54	41
adult organism	1.73e-54	115
neural plate	2.55e-53	86
presumptive neural plate	2.55e-53	86
anterior neural tube	5.27e-53	42
neurectoderm	4.75e-50	90
gray matter	3.85e-45	34
brain grey matter	3.85e-45	34
telencephalon	7.80e-45	34
pre-chordal neural plate	2.02e-43	61
regional part of telencephalon	2.43e-43	33
cerebral hemisphere	5.35e-42	32
ectoderm-derived structure	3.60e-39	169
ectoderm	1.06e-37	173
presumptive ectoderm	1.06e-37	173
head	5.95e-37	123
anterior region of body	8.34e-37	129
craniocervical region	8.34e-37	129
regional part of cerebral cortex	3.17e-34	22
cerebral cortex	7.15e-32	25
pallium	7.15e-32	25
neocortex	2.00e-31	20
posterior neural tube	2.56e-15	15
chordal neural plate	2.56e-15	15
nucleus of brain	1.30e-14	9
neural nucleus	1.30e-14	9
basal ganglion	1.92e-14	9
nuclear complex of neuraxis	1.92e-14	9
aggregate regional part of brain	1.92e-14	9
collection of basal ganglia	1.92e-14	9
cerebral subcortex	1.92e-14	9
tube	5.65e-13	194
temporal lobe	5.75e-13	7
segmental subdivision of nervous system	1.87e-12	13
telencephalic nucleus	1.92e-11	7
segmental subdivision of hindbrain	3.34e-11	12
hindbrain	3.34e-11	12
presumptive hindbrain	3.34e-11	12
diencephalon	5.62e-11	7
future diencephalon	5.62e-11	7
brainstem	1.28e-10	8
gyrus	1.86e-10	6
epithelium	1.04e-09	309
cell layer	1.98e-09	312
organism subdivision	2.69e-09	365
organ part	2.70e-09	219
anatomical conduit	3.15e-09	241
limbic system	7.13e-09	5
parietal lobe	1.56e-08	5
occipital lobe	1.59e-08	5
anatomical cluster	4.01e-08	286
corpus striatum	3.61e-07	4
striatum	3.61e-07	4
ventral part of telencephalon	3.61e-07	4
future corpus striatum	3.61e-07	4
organ	4.00e-07	511
regional part of metencephalon	4.89e-07	9
metencephalon	4.89e-07	9
future metencephalon	4.89e-07	9

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.