Coexpression cluster:C3109

Full id: C3109_skeletal_occipital_temporal_postcentral_paracentral_insula_parietal

Phase1 CAGE Peaks

Hg19::chr11:123525613..123525633,-	p6@SCN3B
Hg19::chr17:37353856..37353900,-	p1@CACNB1
Hg19::chr17:37353907..37353930,-	p2@CACNB1

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:0022843	voltage-gated cation channel activity	0.00153206738976007
GO:0005244	voltage-gated ion channel activity	0.00153206738976007
GO:0022832	voltage-gated channel activity	0.00153206738976007
GO:0005261	cation channel activity	0.00187461200335429
GO:0046873	metal ion transmembrane transporter activity	0.00187461200335429
GO:0022836	gated channel activity	0.00187461200335429
GO:0005216	ion channel activity	0.00195450256590777
GO:0030001	metal ion transport	0.00195450256590777
GO:0022838	substrate specific channel activity	0.00195450256590777
GO:0015267	channel activity	0.00195450256590777
GO:0022803	passive transmembrane transporter activity	0.00195450256590777
GO:0006812	cation transport	0.00257593431578316
GO:0008324	cation transmembrane transporter activity	0.00257593431578316
GO:0005248	voltage-gated sodium channel activity	0.0047167129409244
GO:0015075	ion transmembrane transporter activity	0.00513488797003193
GO:0006811	ion transport	0.00513488797003193
GO:0022891	substrate-specific transmembrane transporter activity	0.00600986352552187
GO:0005891	voltage-gated calcium channel complex	0.00616847909776799
GO:0022857	transmembrane transporter activity	0.00621379523318357
GO:0022892	substrate-specific transporter activity	0.00688725467743432
GO:0005272	sodium channel activity	0.00814285141353296
GO:0005245	voltage-gated calcium channel activity	0.00913501136980657
GO:0031402	sodium ion binding	0.0125145366795723
GO:0005262	calcium channel activity	0.014861404268176
GO:0003012	muscle system process	0.0190081598302255
GO:0006936	muscle contraction	0.0190081598302255
GO:0006814	sodium ion transport	0.0191893628056703
GO:0006816	calcium ion transport	0.0195707371948487
GO:0005886	plasma membrane	0.0221460263117811
GO:0031420	alkali metal ion binding	0.0221460263117811
GO:0006810	transport	0.0228914222139489
GO:0015674	di-, tri-valent inorganic cation transport	0.0228914222139489
GO:0051234	establishment of localization	0.0228914222139489
GO:0051179	localization	0.0260924446112384
GO:0015672	monovalent inorganic cation transport	0.0449431125566352

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	2.52e-23	82
regional part of nervous system	1.29e-21	94
nervous system	1.29e-21	94
neural tube	1.31e-21	57
neural rod	1.31e-21	57
future spinal cord	1.31e-21	57
neural keel	1.31e-21	57
brain	4.56e-20	69
future brain	4.56e-20	69
regional part of brain	1.12e-18	59
ectoderm-derived structure	2.29e-17	169
regional part of forebrain	3.32e-17	41
forebrain	3.32e-17	41
future forebrain	3.32e-17	41
adult organism	4.60e-17	115
neural plate	5.72e-17	86
presumptive neural plate	5.72e-17	86
telencephalon	6.63e-17	34
gray matter	7.42e-17	34
brain grey matter	7.42e-17	34
anterior neural tube	8.59e-17	42
cerebral hemisphere	1.32e-16	32
ectoderm	1.61e-16	173
presumptive ectoderm	1.61e-16	173
regional part of telencephalon	3.03e-16	33
anterior region of body	3.94e-16	129
craniocervical region	3.94e-16	129
neurectoderm	1.24e-15	90
head	2.26e-14	123
regional part of cerebral cortex	1.08e-13	22
cerebral cortex	9.28e-13	25
pallium	9.28e-13	25
organism subdivision	1.25e-12	365
neocortex	1.63e-12	20
pre-chordal neural plate	2.00e-11	61
epithelium	1.47e-08	309
cell layer	2.99e-08	312
multi-tissue structure	4.38e-07	347
organ part	8.73e-07	219

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.