Coexpression cluster:C1130

Full id: C1130_optic_globus_thalamus_spinal_occipital_locus_pons

Phase1 CAGE Peaks

Hg19::chr11:111848024..111848087,+	p1@DIXDC1
Hg19::chr1:78245303..78245351,+	p1@FAM73A
Hg19::chr20:16554078..16554113,-	p2@KIF16B
Hg19::chr2:73053126..73053184,-	p1@EXOC6B
Hg19::chr5:139487363..139487444,+	p1@PURA
Hg19::chr5:139487608..139487663,+	p3@PURA
Hg19::chr6:126112074..126112144,+	p1@NCOA7

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:0003691	double-stranded telomeric DNA binding	0.0250906422742618
GO:0005662	DNA replication factor A complex	0.0250906422742618
GO:0000784	nuclear chromosome, telomeric region	0.0250906422742618
GO:0043601	nuclear replisome	0.0250906422742618
GO:0030894	replisome	0.0250906422742618
GO:0000145	exocyst	0.0250906422742618
GO:0042162	telomeric DNA binding	0.0250906422742618
GO:0046332	SMAD binding	0.0250906422742618
GO:0006268	DNA unwinding during replication	0.0250906422742618
GO:0043596	nuclear replication fork	0.0250906422742618
GO:0032392	DNA geometric change	0.0250906422742618
GO:0032508	DNA duplex unwinding	0.0250906422742618
GO:0016998	cell wall catabolic process	0.0250906422742618
GO:0010382	cell wall metabolic process	0.0250906422742618
GO:0007047	cell wall organization and biogenesis	0.0250906422742618
GO:0045229	external encapsulating structure organization and biogenesis	0.025871678251679
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0298750678121566
GO:0000781	chromosome, telomeric region	0.0310576474269521
GO:0005657	replication fork	0.0310576474269521
GO:0006904	vesicle docking during exocytosis	0.0310576474269521
GO:0006270	DNA replication initiation	0.0310576474269521
GO:0048278	vesicle docking	0.0310576474269521
GO:0022406	membrane docking	0.0310576474269521
GO:0044448	cell cortex part	0.0352318202835125
GO:0003697	single-stranded DNA binding	0.0458051730286997
GO:0005938	cell cortex	0.0462013451222497
GO:0044454	nuclear chromosome part	0.0465674358244908

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
adult organism	2.07e-44	115
neural tube	1.36e-25	57
neural rod	1.36e-25	57
future spinal cord	1.36e-25	57
neural keel	1.36e-25	57
regional part of brain	1.11e-23	59
anterior neural tube	3.21e-22	42
regional part of forebrain	9.41e-22	41
forebrain	9.41e-22	41
future forebrain	9.41e-22	41
brain	3.26e-21	69
future brain	3.26e-21	69
central nervous system	1.21e-18	82
neural plate	4.67e-18	86
presumptive neural plate	4.67e-18	86
telencephalon	9.33e-18	34
gray matter	9.44e-18	34
brain grey matter	9.44e-18	34
neurectoderm	1.52e-17	90
regional part of nervous system	2.99e-17	94
nervous system	2.99e-17	94
regional part of telencephalon	4.01e-17	33
cerebral hemisphere	1.86e-16	32
anterior region of body	4.08e-16	129
craniocervical region	4.08e-16	129
head	5.08e-16	123
regional part of cerebral cortex	8.49e-14	22
neocortex	1.38e-12	20
ectoderm-derived structure	2.23e-12	169
ectoderm	2.86e-12	173
presumptive ectoderm	2.86e-12	173
cerebral cortex	3.96e-12	25
pallium	3.96e-12	25
pre-chordal neural plate	1.06e-11	61
anatomical conduit	5.26e-10	241
anatomical cluster	1.17e-09	286
organism subdivision	3.11e-09	365
tube	6.60e-08	194
nucleus of brain	2.86e-07	9
neural nucleus	2.86e-07	9
basal ganglion	3.48e-07	9
nuclear complex of neuraxis	3.48e-07	9
aggregate regional part of brain	3.48e-07	9
collection of basal ganglia	3.48e-07	9
cerebral subcortex	3.48e-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.