Coexpression cluster:C4395

Full id: C4395_putamen_pituitary_frontal_caudate_amygdala_nucleus_cerebral

Phase1 CAGE Peaks

Hg19::chr4:175750301..175750313,-	p2@GLRA3
Hg19::chr4:176828294..176828305,-	p31@GPM6A
Hg19::chr5:156772645..156772690,-	p1@FNDC9

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:0016934	extracellular-glycine-gated chloride channel activity	0.00824159647213382
GO:0016933	extracellular-glycine-gated ion channel activity	0.00824159647213382
GO:0004890	GABA-A receptor activity	0.0283886005769037
GO:0016917	GABA receptor activity	0.0283886005769037
GO:0043168	anion binding	0.0283886005769037
GO:0031404	chloride ion binding	0.0283886005769037
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0283886005769037
GO:0044459	plasma membrane part	0.0283886005769037
GO:0005254	chloride channel activity	0.0283886005769037
GO:0006821	chloride transport	0.0283886005769037
GO:0005253	anion channel activity	0.0283886005769037
GO:0005230	extracellular ligand-gated ion channel activity	0.0283886005769037
GO:0030594	neurotransmitter receptor activity	0.0283886005769037
GO:0042165	neurotransmitter binding	0.0283886005769037
GO:0009986	cell surface	0.0283886005769037
GO:0045211	postsynaptic membrane	0.0283886005769037
GO:0044456	synapse part	0.0283886005769037
GO:0015276	ligand-gated ion channel activity	0.0283886005769037
GO:0022834	ligand-gated channel activity	0.0283886005769037
GO:0008509	anion transmembrane transporter activity	0.0336389316043571
GO:0005886	plasma membrane	0.0336389316043571
GO:0015698	inorganic anion transport	0.0388140398722077
GO:0007268	synaptic transmission	0.0413919419054682
GO:0006820	anion transport	0.0433074604608263
GO:0019226	transmission of nerve impulse	0.0433074604608263

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	6.33e-110	56
neural rod	6.33e-110	56
future spinal cord	6.33e-110	56
neural keel	6.33e-110	56
regional part of nervous system	2.25e-98	53
regional part of brain	2.25e-98	53
central nervous system	4.39e-86	81
regional part of forebrain	5.70e-82	41
forebrain	5.70e-82	41
anterior neural tube	5.70e-82	41
future forebrain	5.70e-82	41
brain	6.04e-79	68
future brain	6.04e-79	68
nervous system	6.74e-77	89
neural plate	4.24e-73	82
presumptive neural plate	4.24e-73	82
telencephalon	1.26e-72	34
brain grey matter	1.92e-72	34
gray matter	1.92e-72	34
cerebral hemisphere	4.26e-71	32
neurectoderm	2.19e-69	86
regional part of telencephalon	7.80e-65	32
regional part of cerebral cortex	3.93e-63	22
ecto-epithelium	3.61e-56	104
cerebral cortex	2.39e-55	25
pallium	2.39e-55	25
neocortex	1.30e-54	20
pre-chordal neural plate	1.96e-53	61
adult organism	3.12e-51	114
structure with developmental contribution from neural crest	2.40e-45	132
ectoderm-derived structure	6.35e-37	171
ectoderm	6.35e-37	171
presumptive ectoderm	6.35e-37	171
organ system subdivision	4.24e-28	223
posterior neural tube	2.24e-27	15
chordal neural plate	2.24e-27	15
tube	5.36e-27	192
temporal lobe	2.47e-24	6
limbic system	3.02e-24	5
gyrus	4.77e-20	6
anatomical conduit	4.79e-20	240
basal ganglion	7.35e-19	9
nuclear complex of neuraxis	7.35e-19	9
aggregate regional part of brain	7.35e-19	9
collection of basal ganglia	7.35e-19	9
cerebral subcortex	7.35e-19	9
brainstem	3.26e-18	6
neural nucleus	4.33e-18	9
nucleus of brain	4.33e-18	9
segmental subdivision of hindbrain	4.76e-17	12
hindbrain	4.76e-17	12
presumptive hindbrain	4.76e-17	12
segmental subdivision of nervous system	1.14e-15	13
parietal lobe	1.77e-15	5
epithelium	5.02e-14	306
spinal cord	7.24e-14	3
dorsal region element	7.24e-14	3
dorsum	7.24e-14	3
cell layer	8.20e-14	309
pons	1.08e-13	3
anatomical cluster	1.23e-13	373
organ part	1.90e-12	218
regional part of metencephalon	6.08e-12	9
metencephalon	6.08e-12	9
future metencephalon	6.08e-12	9
corpus striatum	1.28e-11	4
striatum	1.28e-11	4
ventral part of telencephalon	1.28e-11	4
future corpus striatum	1.28e-11	4
telencephalic nucleus	4.30e-11	7
amygdala	5.03e-11	2
middle temporal gyrus	7.77e-11	2
diencephalon	9.34e-11	7
future diencephalon	9.34e-11	7
pituitary gland	1.25e-10	2
Ammon's horn	1.38e-10	2
lobe parts of cerebral cortex	1.38e-10	2
hippocampal formation	1.38e-10	2
limbic lobe	1.38e-10	2
multi-tissue structure	6.24e-10	342
locus ceruleus	7.68e-10	2
brainstem nucleus	7.68e-10	2
hindbrain nucleus	7.68e-10	2
occipital lobe	5.38e-09	5
caudate-putamen	1.47e-07	3
dorsal striatum	1.47e-07	3
frontal cortex	1.62e-07	3
organ	3.02e-07	503
medulla oblongata	6.72e-07	3
myelencephalon	6.72e-07	3
future myelencephalon	6.72e-07	3

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.