Coexpression cluster:C3331

Full id: C3331_brain_occipital_paracentral_parietal_insula_postcentral_pons

Phase1 CAGE Peaks

Hg19::chr12:75603643..75603652,-	p19@KCNC2
Hg19::chr1:116915494..116915499,+	p52@ATP1A1
Hg19::chr7:152456920..152456929,+	p4@ACTR3B

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:0030955	potassium ion binding	0.00539806025887904
GO:0031420	alkali metal ion binding	0.00585347486191332
GO:0006813	potassium ion transport	0.00585347486191332
GO:0005890	sodium:potassium-exchanging ATPase complex	0.0148899497119923
GO:0015672	monovalent inorganic cation transport	0.0148899497119923
GO:0030641	cellular hydrogen ion homeostasis	0.0153004158396385
GO:0030001	metal ion transport	0.0153004158396385
GO:0055067	monovalent inorganic cation homeostasis	0.0153004158396385
GO:0030004	cellular monovalent inorganic cation homeostasis	0.0153004158396385
GO:0005391	sodium:potassium-exchanging ATPase activity	0.01548990470091
GO:0030317	sperm motility	0.01548990470091
GO:0006812	cation transport	0.01548990470091
GO:0008324	cation transmembrane transporter activity	0.01548990470091
GO:0015075	ion transmembrane transporter activity	0.0287753110400164
GO:0005887	integral to plasma membrane	0.0287753110400164
GO:0031226	intrinsic to plasma membrane	0.0287753110400164
GO:0006811	ion transport	0.0287753110400164
GO:0022891	substrate-specific transmembrane transporter activity	0.0336885223102745
GO:0022857	transmembrane transporter activity	0.0362112514340256
GO:0048770	pigment granule	0.0362112514340256
GO:0042470	melanosome	0.0362112514340256
GO:0022892	substrate-specific transporter activity	0.0369774297685521
GO:0031402	sodium ion binding	0.0382262584592676
GO:0008076	voltage-gated potassium channel complex	0.0468993386301315

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	4.42e-22	82
regional part of nervous system	1.06e-21	94
nervous system	1.06e-21	94
neural tube	1.23e-21	57
neural rod	1.23e-21	57
future spinal cord	1.23e-21	57
neural keel	1.23e-21	57
brain	9.74e-21	69
future brain	9.74e-21	69
regional part of brain	6.33e-19	59
telencephalon	8.43e-19	34
cerebral hemisphere	9.34e-19	32
regional part of forebrain	1.01e-18	41
forebrain	1.01e-18	41
future forebrain	1.01e-18	41
gray matter	1.82e-18	34
brain grey matter	1.82e-18	34
anterior neural tube	4.83e-18	42
regional part of telencephalon	1.10e-17	33
neural plate	4.33e-16	86
presumptive neural plate	4.33e-16	86
neurectoderm	1.32e-15	90
cerebral cortex	1.32e-15	25
pallium	1.32e-15	25
regional part of cerebral cortex	1.38e-14	22
neocortex	1.74e-14	20
pre-chordal neural plate	5.21e-13	61
adult organism	1.48e-11	115
head	5.36e-11	123
anterior region of body	2.56e-10	129
craniocervical region	2.56e-10	129
ectoderm-derived structure	1.86e-09	169
ectoderm	2.30e-09	173
presumptive ectoderm	2.30e-09	173
occipital lobe	1.50e-07	5

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.