Coexpression cluster:C2466

Full id: C2466_pineal_putamen_caudate_nucleus_globus_diencephalon_hippocampus

Phase1 CAGE Peaks

Hg19::chr18:55019685..55019704,+	p3@ST8SIA3
Hg19::chr2:220197419..220197439,-	p2@RESP18
Hg19::chr2:220197453..220197472,-	p1@RESP18
Hg19::chr4:786267..786295,-	p3@CPLX1

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:0003828	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity	0.0115091906183776
GO:0006491	N-glycan processing	0.0115091906183776
GO:0006688	glycosphingolipid biosynthetic process	0.0115091906183776
GO:0009247	glycolipid biosynthetic process	0.0115091906183776
GO:0019905	syntaxin binding	0.0115091906183776
GO:0006687	glycosphingolipid metabolic process	0.0115091906183776
GO:0000149	SNARE binding	0.0115091906183776
GO:0030148	sphingolipid biosynthetic process	0.0115091906183776
GO:0009311	oligosaccharide metabolic process	0.0115091906183776
GO:0006664	glycolipid metabolic process	0.013652678031185
GO:0008373	sialyltransferase activity	0.0162612229872916
GO:0006487	protein amino acid N-linked glycosylation	0.020785523760556
GO:0030173	integral to Golgi membrane	0.0219565634295245
GO:0006665	sphingolipid metabolic process	0.0219565634295245
GO:0031228	intrinsic to Golgi membrane	0.0219565634295245
GO:0006836	neurotransmitter transport	0.0229340636616927
GO:0006887	exocytosis	0.0295180929314387
GO:0046467	membrane lipid biosynthetic process	0.0295180929314387
GO:0031301	integral to organelle membrane	0.0343856354656499
GO:0031300	intrinsic to organelle membrane	0.035714631449367
GO:0006486	protein amino acid glycosylation	0.0371692586264835
GO:0043413	biopolymer glycosylation	0.0371692586264835
GO:0009101	glycoprotein biosynthetic process	0.0371692586264835
GO:0009100	glycoprotein metabolic process	0.040693567841378
GO:0045045	secretory pathway	0.0450546568690579
GO:0006643	membrane lipid metabolic process	0.0490748172019442
GO:0007268	synaptic transmission	0.0497394615442673
GO:0032940	secretion by cell	0.0497394615442673

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	7.18e-43	57
neural rod	7.18e-43	57
future spinal cord	7.18e-43	57
neural keel	7.18e-43	57
regional part of nervous system	2.09e-42	94
nervous system	2.09e-42	94
central nervous system	1.85e-41	82
adult organism	1.03e-37	115
neural plate	1.00e-36	86
presumptive neural plate	1.00e-36	86
brain	2.36e-35	69
future brain	2.36e-35	69
regional part of brain	5.06e-35	59
neurectoderm	8.75e-35	90
regional part of forebrain	3.46e-34	41
forebrain	3.46e-34	41
future forebrain	3.46e-34	41
anterior neural tube	6.83e-33	42
pre-chordal neural plate	7.17e-29	61
gray matter	4.10e-28	34
brain grey matter	4.10e-28	34
telencephalon	6.32e-28	34
regional part of telencephalon	4.43e-27	33
cerebral hemisphere	1.16e-26	32
ectoderm-derived structure	3.52e-25	169
anterior region of body	4.73e-25	129
craniocervical region	4.73e-25	129
ectoderm	2.07e-24	173
presumptive ectoderm	2.07e-24	173
head	6.96e-24	123
cerebral cortex	2.87e-20	25
pallium	2.87e-20	25
regional part of cerebral cortex	8.36e-20	22
neocortex	5.24e-18	20
organ part	1.98e-13	219
tube	2.87e-13	194
anatomical conduit	2.97e-13	241
anatomical cluster	1.38e-11	286
posterior neural tube	6.97e-11	15
chordal neural plate	6.97e-11	15
multi-tissue structure	2.17e-10	347
epithelium	3.97e-10	309
cell layer	1.10e-09	312
basal ganglion	2.39e-09	9
nuclear complex of neuraxis	2.39e-09	9
aggregate regional part of brain	2.39e-09	9
collection of basal ganglia	2.39e-09	9
cerebral subcortex	2.39e-09	9
organism subdivision	2.44e-09	365
segmental subdivision of nervous system	2.53e-09	13
nucleus of brain	2.69e-09	9
neural nucleus	2.69e-09	9
segmental subdivision of hindbrain	7.75e-09	12
hindbrain	7.75e-09	12
presumptive hindbrain	7.75e-09	12
temporal lobe	9.82e-08	7
diencephalon	1.22e-07	7
future diencephalon	1.22e-07	7
telencephalic nucleus	1.36e-07	7

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.