Coexpression cluster:C1049

Full id: C1049_pineal_medial_hippocampus_middle_occipital_amygdala_parietal

Phase1 CAGE Peaks

Hg19::chr17:38438270..38438296,+	p@chr17:38438270..38438296 +
Hg19::chr17:8063552..8063607,-	p9@VAMP2
Hg19::chr17:8063738..8063750,-	p12@VAMP2
Hg19::chr17:8063830..8063875,-	p8@VAMP2
Hg19::chr19:42470916..42470937,-	p@chr19:42470916..42470937 -
Hg19::chr1:222791157..222791168,+	p10@MIA3
Hg19::chr2:210598049..210598077,+	p@chr2:210598049..210598077 +
Hg19::chr2:210598112..210598127,+	p@chr2:210598112..210598127 +

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:0002687	positive regulation of leukocyte migration	0.00185446838572942
GO:0002685	regulation of leukocyte migration	0.00185446838572942
GO:0030335	positive regulation of cell migration	0.0107107636356278
GO:0030336	negative regulation of cell migration	0.0107107636356278
GO:0051272	positive regulation of cell motility	0.0107107636356278
GO:0040017	positive regulation of locomotion	0.0107107636356278
GO:0051271	negative regulation of cell motility	0.0107107636356278
GO:0040013	negative regulation of locomotion	0.0107107636356278
GO:0007162	negative regulation of cell adhesion	0.0107107636356278
GO:0050900	leukocyte migration	0.011492627144804
GO:0019717	synaptosome	0.012132085517086
GO:0030334	regulation of cell migration	0.0169040912870174
GO:0030155	regulation of cell adhesion	0.0169040912870174
GO:0051270	regulation of cell motility	0.0169040912870174
GO:0040012	regulation of locomotion	0.0169040912870174
GO:0040011	locomotion	0.0169040912870174
GO:0002684	positive regulation of immune system process	0.0187393830162024
GO:0002682	regulation of immune system process	0.0204653811019412
GO:0051240	positive regulation of multicellular organismal process	0.0204653811019412
GO:0042060	wound healing	0.0242470526812193
GO:0016477	cell migration	0.0410110173448688
GO:0051239	regulation of multicellular organismal process	0.0465091813705923
GO:0051179	localization	0.0476470727683483

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	3.48e-28	57
neural rod	3.48e-28	57
future spinal cord	3.48e-28	57
neural keel	3.48e-28	57
central nervous system	5.29e-27	82
adult organism	1.13e-25	115
regional part of nervous system	1.35e-25	94
nervous system	1.35e-25	94
anterior neural tube	1.05e-23	42
regional part of forebrain	2.56e-23	41
forebrain	2.56e-23	41
future forebrain	2.56e-23	41
brain	3.97e-22	69
future brain	3.97e-22	69
regional part of brain	8.03e-22	59
neurectoderm	1.58e-21	90
neural plate	1.55e-20	86
presumptive neural plate	1.55e-20	86
gray matter	2.52e-19	34
brain grey matter	2.52e-19	34
telencephalon	4.56e-19	34
regional part of telencephalon	1.67e-18	33
cerebral hemisphere	4.22e-18	32
regional part of cerebral cortex	1.35e-15	22
pre-chordal neural plate	4.74e-15	61
neocortex	3.03e-14	20
cerebral cortex	5.84e-14	25
pallium	5.84e-14	25
ectoderm	8.13e-14	173
presumptive ectoderm	8.13e-14	173
ectoderm-derived structure	5.57e-13	169
anterior region of body	1.08e-08	129
craniocervical region	1.08e-08	129
head	1.49e-08	123
basal ganglion	5.63e-07	9
nuclear complex of neuraxis	5.63e-07	9
aggregate regional part of brain	5.63e-07	9
collection of basal ganglia	5.63e-07	9
cerebral subcortex	5.63e-07	9
nucleus of brain	7.14e-07	9
neural nucleus	7.14e-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.