Coexpression cluster:C1303

Full id: C1303_hippocampus_pituitary_insula_medulla_medial_occipital_paracentral

Phase1 CAGE Peaks

Hg19::chr10:125425217..125425232,+	p@chr10:125425217..125425232 +
Hg19::chr11:81359062..81359117,-	p@chr11:81359062..81359117 -
Hg19::chr11:81359124..81359143,-	p@chr11:81359124..81359143 -
Hg19::chr11:81359178..81359208,-	p@chr11:81359178..81359208 -
Hg19::chr6:152793728..152793766,-	p14@SYNE1
Hg19::chrX:151619719..151619724,-	p3@GABRA3

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:0045211	postsynaptic membrane	0.000948648538551125
GO:0044456	synapse part	0.000948648538551125
GO:0005521	lamin binding	0.00875643846671322
GO:0008503	benzodiazepine receptor activity	0.00875643846671322
GO:0007030	Golgi organization and biogenesis	0.014008857951139
GO:0007214	gamma-aminobutyric acid signaling pathway	0.0216765454530563
GO:0006997	nuclear organization and biogenesis	0.0235034451487031
GO:0004890	GABA-A receptor activity	0.0235034451487031
GO:0042692	muscle cell differentiation	0.0235034451487031
GO:0016917	GABA receptor activity	0.0235034451487031
GO:0043168	anion binding	0.0249988776174169
GO:0031404	chloride ion binding	0.0249988776174169
GO:0005254	chloride channel activity	0.0310576757163792
GO:0006821	chloride transport	0.0310576757163792
GO:0005253	anion channel activity	0.0333121960667309
GO:0005230	extracellular ligand-gated ion channel activity	0.0389860458602887
GO:0030594	neurotransmitter receptor activity	0.0389860458602887
GO:0042165	neurotransmitter binding	0.0389860458602887
GO:0031965	nuclear membrane	0.0389860458602887
GO:0015276	ligand-gated ion channel activity	0.0389860458602887
GO:0022834	ligand-gated channel activity	0.0389860458602887
GO:0005635	nuclear envelope	0.0440018987458718
GO:0008509	anion transmembrane transporter activity	0.0453330200615595

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	1.78e-100	56
neural rod	1.78e-100	56
future spinal cord	1.78e-100	56
neural keel	1.78e-100	56
regional part of nervous system	1.16e-91	53
regional part of brain	1.16e-91	53
central nervous system	8.06e-91	81
regional part of forebrain	8.43e-86	41
forebrain	8.43e-86	41
anterior neural tube	8.43e-86	41
future forebrain	8.43e-86	41
brain	6.90e-84	68
future brain	6.90e-84	68
nervous system	8.51e-81	89
telencephalon	1.60e-80	34
brain grey matter	1.75e-80	34
gray matter	1.75e-80	34
cerebral hemisphere	4.98e-75	32
regional part of telencephalon	2.55e-74	32
neural plate	7.51e-69	82
presumptive neural plate	7.51e-69	82
regional part of cerebral cortex	4.96e-68	22
neurectoderm	3.49e-65	86
neocortex	3.81e-61	20
cerebral cortex	1.80e-59	25
pallium	1.80e-59	25
pre-chordal neural plate	1.47e-58	61
ecto-epithelium	9.62e-55	104
adult organism	1.39e-54	114
structure with developmental contribution from neural crest	4.58e-43	132
ectoderm-derived structure	8.62e-41	171
ectoderm	8.62e-41	171
presumptive ectoderm	8.62e-41	171
organ system subdivision	6.77e-33	223
tube	9.51e-25	192
basal ganglion	5.37e-22	9
nuclear complex of neuraxis	5.37e-22	9
aggregate regional part of brain	5.37e-22	9
collection of basal ganglia	5.37e-22	9
cerebral subcortex	5.37e-22	9
neural nucleus	7.56e-22	9
nucleus of brain	7.56e-22	9
gyrus	3.06e-21	6
brainstem	8.55e-20	6
anatomical conduit	1.06e-18	240
limbic system	6.83e-18	5
parietal lobe	1.89e-17	5
temporal lobe	4.10e-17	6
occipital lobe	6.54e-17	5
anatomical cluster	9.23e-17	373
posterior neural tube	2.16e-16	15
chordal neural plate	2.16e-16	15
telencephalic nucleus	5.87e-16	7
epithelium	5.26e-14	306
cell layer	9.23e-14	309
frontal cortex	1.95e-11	3
organ part	4.45e-11	218
pons	8.65e-11	3
medulla oblongata	9.88e-11	3
myelencephalon	9.88e-11	3
future myelencephalon	9.88e-11	3
multi-tissue structure	1.33e-10	342
spinal cord	2.04e-10	3
dorsal region element	2.04e-10	3
dorsum	2.04e-10	3
organ	7.69e-10	503
segmental subdivision of hindbrain	1.51e-09	12
hindbrain	1.51e-09	12
presumptive hindbrain	1.51e-09	12
segmental subdivision of nervous system	9.29e-09	13
Ammon's horn	1.73e-08	2
lobe parts of cerebral cortex	1.73e-08	2
hippocampal formation	1.73e-08	2
limbic lobe	1.73e-08	2
pituitary gland	2.00e-08	2
middle frontal gyrus	3.50e-08	2
middle temporal gyrus	4.30e-08	2
corpus striatum	5.21e-08	4
striatum	5.21e-08	4
ventral part of telencephalon	5.21e-08	4
future corpus striatum	5.21e-08	4
diencephalon	5.70e-08	7
future diencephalon	5.70e-08	7
amygdala	6.50e-08	2
locus ceruleus	9.75e-08	2
brainstem nucleus	9.75e-08	2
hindbrain nucleus	9.75e-08	2
embryo	1.20e-07	592
germ layer	1.64e-07	560
germ layer / neural crest	1.64e-07	560
embryonic tissue	1.64e-07	560
presumptive structure	1.64e-07	560
germ layer / neural crest derived structure	1.64e-07	560
epiblast (generic)	1.64e-07	560
developing anatomical structure	2.07e-07	581
embryonic structure	2.29e-07	564
globus pallidus	2.54e-07	2
pallidum	2.54e-07	2
dorsal plus ventral thalamus	3.19e-07	2
thalamic complex	3.19e-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.