Coexpression cluster:C1050

Full id: C1050_brain_diencephalon_substantia_corpus_occipital_optic_spinal

Phase1 CAGE Peaks

Hg19::chr17:40123919..40123952,+	p6@CNP
Hg19::chr17:56598639..56598652,-	p@chr17:56598639..56598652 -
Hg19::chr19:36362881..36362902,+	p@chr19:36362881..36362902 +
Hg19::chr19:36367441..36367488,+	p@chr19:36367441..36367488 +
Hg19::chr19:36370032..36370046,+	p@chr19:36370032..36370046 +
Hg19::chr2:128403581..128403584,+	p6@GPR17
Hg19::chr2:233740296..233740309,+	p10@C2orf82
Hg19::chr2:96686244..96686248,+	p@chr2:96686244..96686248 +

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:0004113	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity	0.0041209802018991
GO:0009214	cyclic nucleotide catabolic process	0.0041209802018991
GO:0009166	nucleotide catabolic process	0.017158619785766
GO:0001637	G-protein chemoattractant receptor activity	0.017158619785766
GO:0004950	chemokine receptor activity	0.017158619785766
GO:0019956	chemokine binding	0.017158619785766
GO:0001608	nucleotide receptor activity, G-protein coupled	0.017158619785766
GO:0045028	purinergic nucleotide receptor activity, G-protein coupled	0.017158619785766
GO:0016502	nucleotide receptor activity	0.017158619785766
GO:0001614	purinergic nucleotide receptor activity	0.017158619785766
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.017158619785766
GO:0009187	cyclic nucleotide metabolic process	0.017158619785766
GO:0048770	pigment granule	0.0244023979519757
GO:0042470	melanosome	0.0244023979519757
GO:0019955	cytokine binding	0.027159637823942
GO:0008081	phosphoric diester hydrolase activity	0.0338108017026104
GO:0001653	peptide receptor activity	0.0338108017026104
GO:0008528	peptide receptor activity, G-protein coupled	0.0338108017026104
GO:0042277	peptide binding	0.0449771012983651

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
regional part of nervous system	3.30e-35	94
nervous system	3.30e-35	94
central nervous system	3.39e-33	82
neural tube	1.56e-31	57
neural rod	1.56e-31	57
future spinal cord	1.56e-31	57
neural keel	1.56e-31	57
neurectoderm	2.99e-30	90
neural plate	3.68e-29	86
presumptive neural plate	3.68e-29	86
brain	3.08e-26	69
future brain	3.08e-26	69
regional part of brain	1.18e-25	59
regional part of forebrain	2.82e-24	41
forebrain	2.82e-24	41
future forebrain	2.82e-24	41
ectoderm	3.99e-24	173
presumptive ectoderm	3.99e-24	173
ectoderm-derived structure	4.97e-23	169
anterior neural tube	5.12e-23	42
pre-chordal neural plate	1.29e-20	61
telencephalon	3.01e-20	34
gray matter	3.09e-20	34
brain grey matter	3.09e-20	34
adult organism	7.25e-20	115
regional part of telencephalon	1.29e-19	33
cerebral hemisphere	8.15e-19	32
head	1.06e-18	123
anterior region of body	4.62e-18	129
craniocervical region	4.62e-18	129
cerebral cortex	2.63e-14	25
pallium	2.63e-14	25
regional part of cerebral cortex	8.62e-14	22
neocortex	1.67e-12	20
tube	7.44e-10	194
posterior neural tube	1.37e-09	15
chordal neural plate	1.37e-09	15
epithelium	1.69e-09	309
cell layer	2.09e-09	312
organism subdivision	1.07e-08	365
anatomical conduit	1.75e-08	241
segmental subdivision of nervous system	2.70e-08	13
segmental subdivision of hindbrain	1.30e-07	12
hindbrain	1.30e-07	12
presumptive hindbrain	1.30e-07	12
organ part	1.70e-07	219
nucleus of brain	1.78e-07	9
neural nucleus	1.78e-07	9
basal ganglion	2.12e-07	9
nuclear complex of neuraxis	2.12e-07	9
aggregate regional part of brain	2.12e-07	9
collection of basal ganglia	2.12e-07	9
cerebral subcortex	2.12e-07	9
anatomical cluster	3.57e-07	286

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.