Coexpression cluster:C1179

Full id: C1179_parietal_putamen_occipital_medial_caudate_hippocampus_amygdala

Phase1 CAGE Peaks

Hg19::chr12:87232771..87232788,-	p2@ENST00000550014
Hg19::chr19:55946950..55946958,-	p@chr19:55946950..55946958 -
Hg19::chr2:166060606..166060607,-	p6@SCN3A
Hg19::chr2:175708423..175708427,-	p@chr2:175708423..175708427 -
Hg19::chr3:116303353..116303355,-	p@chr3:116303353..116303355 -
Hg19::chr3:116818981..116818985,-	p@chr3:116818981..116818985 -
Hg19::chr3:116997189..116997193,-	p@chr3:116997189..116997193 -

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:0001518	voltage-gated sodium channel complex	0.0135994348286824
GO:0005248	voltage-gated sodium channel activity	0.0135994348286824
GO:0005272	sodium channel activity	0.023489932885906
GO:0031402	sodium ion binding	0.0296714941716708
GO:0006814	sodium ion transport	0.0427764040974921
GO:0031420	alkali metal ion binding	0.0443698732289336
GO:0022843	voltage-gated cation channel activity	0.0443698732289336
GO:0005244	voltage-gated ion channel activity	0.0443698732289336
GO:0022832	voltage-gated channel activity	0.0443698732289336
GO:0005261	cation channel activity	0.0479414419718199
GO:0046873	metal ion transmembrane transporter activity	0.0479414419718199
GO:0022836	gated channel activity	0.0479414419718199
GO:0015672	monovalent inorganic cation transport	0.0479414419718199
GO:0005216	ion channel activity	0.0479414419718199
GO:0030001	metal ion transport	0.0479414419718199
GO:0022838	substrate specific channel activity	0.0479414419718199
GO:0015267	channel activity	0.0479414419718199
GO:0022803	passive transmembrane transporter activity	0.0479414419718199

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	9.14e-94	56
neural rod	9.14e-94	56
future spinal cord	9.14e-94	56
neural keel	9.14e-94	56
regional part of nervous system	4.40e-86	53
regional part of brain	4.40e-86	53
regional part of forebrain	4.67e-74	41
forebrain	4.67e-74	41
anterior neural tube	4.67e-74	41
future forebrain	4.67e-74	41
brain grey matter	3.94e-71	34
gray matter	3.94e-71	34
telencephalon	1.76e-70	34
central nervous system	5.33e-69	81
brain	7.75e-67	68
future brain	7.75e-67	68
nervous system	3.02e-66	89
regional part of telencephalon	5.82e-66	32
cerebral hemisphere	6.58e-66	32
neural plate	3.96e-63	82
presumptive neural plate	3.96e-63	82
neurectoderm	1.26e-59	86
regional part of cerebral cortex	3.61e-50	22
pre-chordal neural plate	1.29e-49	61
ecto-epithelium	1.82e-49	104
cerebral cortex	6.75e-48	25
pallium	6.75e-48	25
adult organism	1.40e-47	114
neocortex	1.06e-44	20
structure with developmental contribution from neural crest	6.93e-40	132
ectoderm-derived structure	1.80e-31	171
ectoderm	1.80e-31	171
presumptive ectoderm	1.80e-31	171
organ system subdivision	4.82e-28	223
basal ganglion	7.35e-25	9
nuclear complex of neuraxis	7.35e-25	9
aggregate regional part of brain	7.35e-25	9
collection of basal ganglia	7.35e-25	9
cerebral subcortex	7.35e-25	9
neural nucleus	1.31e-24	9
nucleus of brain	1.31e-24	9
tube	1.67e-24	192
posterior neural tube	5.57e-20	15
chordal neural plate	5.57e-20	15
telencephalic nucleus	1.39e-19	7
anatomical conduit	6.00e-18	240
gyrus	8.44e-17	6
brainstem	3.64e-16	6
limbic system	7.04e-15	5
temporal lobe	1.86e-14	6
parietal lobe	4.23e-14	5
segmental subdivision of hindbrain	2.48e-13	12
hindbrain	2.48e-13	12
presumptive hindbrain	2.48e-13	12
anatomical cluster	3.48e-13	373
epithelium	9.31e-13	306
cell layer	1.66e-12	309
corpus striatum	3.28e-12	4
striatum	3.28e-12	4
ventral part of telencephalon	3.28e-12	4
future corpus striatum	3.28e-12	4
segmental subdivision of nervous system	3.42e-12	13
organ part	3.56e-12	218
multi-tissue structure	6.04e-10	342
caudate-putamen	9.08e-10	3
dorsal striatum	9.08e-10	3
frontal cortex	9.35e-10	3
occipital lobe	2.62e-09	5
spinal cord	3.78e-09	3
dorsal region element	3.78e-09	3
dorsum	3.78e-09	3
pons	5.69e-09	3
medulla oblongata	6.88e-09	3
myelencephalon	6.88e-09	3
future myelencephalon	6.88e-09	3
embryonic structure	1.01e-07	564
regional part of metencephalon	2.32e-07	9
metencephalon	2.32e-07	9
future metencephalon	2.32e-07	9
germ layer	2.55e-07	560
germ layer / neural crest	2.55e-07	560
embryonic tissue	2.55e-07	560
presumptive structure	2.55e-07	560
germ layer / neural crest derived structure	2.55e-07	560
epiblast (generic)	2.55e-07	560
middle frontal gyrus	3.76e-07	2
embryo	3.86e-07	592
Ammon's horn	3.87e-07	2
lobe parts of cerebral cortex	3.87e-07	2
hippocampal formation	3.87e-07	2
limbic lobe	3.87e-07	2
developing anatomical structure	4.97e-07	581
amygdala	5.78e-07	2
caudate nucleus	5.95e-07	2
future caudate nucleus	5.95e-07	2
middle temporal gyrus	6.48e-07	2
dorsal plus ventral thalamus	9.10e-07	2
thalamic complex	9.10e-07	2

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.