Coexpression cluster:C693

Full id: C693_cerebellum_medulla_spinal_locus_Hepatocyte_pons_thalamus

Phase1 CAGE Peaks

Hg19::chr11:7369947..7369952,+	p@chr11:7369947..7369952 +
Hg19::chr12:109273861..109273889,+	p1@DAO
Hg19::chr19:29493456..29493477,+	p1@LOC100505835
Hg19::chr19:29493486..29493497,+	p2@LOC100505835
Hg19::chr1:90885631..90885647,-	p@chr1:90885631..90885647 -
Hg19::chr1:90885681..90885693,-	p@chr1:90885681..90885693 -
Hg19::chr3:125997081..125997085,+	p@chr3:125997081..125997085 +
Hg19::chr3:147111505..147111529,+	p6@ZIC1
Hg19::chr6:138959791..138959803,-	p@chr6:138959791..138959803 -
Hg19::chr9:73736331..73736347,-	p3@TRPM3
Hg19::chrX:106692537..106692551,+	p@chrX:106692537..106692551 +
Hg19::chrX:106692569..106692585,+	p@chrX:106692569..106692585 +

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:0003884	D-amino-acid oxidase activity	0.0358467233571613
GO:0008589	regulation of smoothened signaling pathway	0.0358467233571613
GO:0007224	smoothened signaling pathway	0.0453250397872941
GO:0016641	oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor	0.0453250397872941
GO:0042472	inner ear morphogenesis	0.0453250397872941
GO:0016638	oxidoreductase activity, acting on the CH-NH2 group of donors	0.0453250397872941
GO:0042471	ear morphogenesis	0.0453250397872941
GO:0048839	inner ear development	0.0477464012889728
GO:0043583	ear development	0.0477464012889728

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	1.47e-114	56
neural rod	1.47e-114	56
future spinal cord	1.47e-114	56
neural keel	1.47e-114	56
regional part of nervous system	1.48e-102	53
regional part of brain	1.48e-102	53
central nervous system	4.46e-93	81
brain	1.69e-86	68
future brain	1.69e-86	68
nervous system	3.88e-83	89
neural plate	4.62e-80	82
presumptive neural plate	4.62e-80	82
neurectoderm	5.39e-76	86
regional part of forebrain	5.50e-73	41
forebrain	5.50e-73	41
anterior neural tube	5.50e-73	41
future forebrain	5.50e-73	41
adult organism	2.68e-65	114
brain grey matter	2.48e-64	34
gray matter	2.48e-64	34
telencephalon	4.87e-64	34
ecto-epithelium	1.60e-61	104
regional part of telencephalon	9.66e-57	32
cerebral hemisphere	1.65e-56	32
structure with developmental contribution from neural crest	4.65e-52	132
pre-chordal neural plate	6.92e-51	61
ectoderm-derived structure	5.51e-42	171
ectoderm	5.51e-42	171
presumptive ectoderm	5.51e-42	171
posterior neural tube	7.28e-42	15
chordal neural plate	7.28e-42	15
neural nucleus	7.39e-38	9
nucleus of brain	7.39e-38	9
regional part of cerebral cortex	1.24e-37	22
cerebral cortex	6.80e-33	25
pallium	6.80e-33	25
neocortex	1.12e-30	20
organ system subdivision	3.19e-30	223
segmental subdivision of hindbrain	7.55e-30	12
hindbrain	7.55e-30	12
presumptive hindbrain	7.55e-30	12
basal ganglion	1.66e-29	9
nuclear complex of neuraxis	1.66e-29	9
aggregate regional part of brain	1.66e-29	9
collection of basal ganglia	1.66e-29	9
cerebral subcortex	1.66e-29	9
telencephalic nucleus	2.16e-29	7
tube	6.60e-28	192
segmental subdivision of nervous system	2.03e-27	13
brainstem	2.43e-27	6
anatomical conduit	1.20e-20	240
regional part of metencephalon	5.64e-18	9
metencephalon	5.64e-18	9
future metencephalon	5.64e-18	9
gyrus	3.62e-17	6
corpus striatum	7.83e-17	4
striatum	7.83e-17	4
ventral part of telencephalon	7.83e-17	4
future corpus striatum	7.83e-17	4
anatomical cluster	1.26e-15	373
epithelium	2.21e-15	306
cell layer	3.78e-15	309
medulla oblongata	7.87e-15	3
myelencephalon	7.87e-15	3
future myelencephalon	7.87e-15	3
spinal cord	2.53e-14	3
dorsal region element	2.53e-14	3
dorsum	2.53e-14	3
pons	2.77e-14	3
limbic system	3.10e-14	5
organ part	4.88e-14	218
caudate-putamen	6.21e-13	3
dorsal striatum	6.21e-13	3
multi-tissue structure	6.88e-11	342
regional part of diencephalon	1.85e-10	4
diencephalon	2.88e-10	7
future diencephalon	2.88e-10	7
locus ceruleus	3.32e-10	2
brainstem nucleus	3.32e-10	2
hindbrain nucleus	3.32e-10	2
globus pallidus	3.63e-10	2
pallidum	3.63e-10	2
dorsal plus ventral thalamus	4.54e-10	2
thalamic complex	4.54e-10	2
Ammon's horn	6.77e-10	2
lobe parts of cerebral cortex	6.77e-10	2
hippocampal formation	6.77e-10	2
limbic lobe	6.77e-10	2
temporal lobe	9.50e-10	6
caudate nucleus	3.98e-09	2
future caudate nucleus	3.98e-09	2
middle temporal gyrus	4.51e-09	2
meninx	5.57e-09	2
membrane organ	5.57e-09	2
meningeal cluster	5.57e-09	2
organ	1.74e-08	503
parietal lobe	4.54e-08	5
occipital lobe	4.66e-08	5
cerebellum	1.39e-07	6
rhombic lip	1.39e-07	6

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.