Coexpression cluster:C1062

Full id: C1062_extraskeletal_pineal_amygdala_middle_medial_parietal_hippocampus

Phase1 CAGE Peaks

Hg19::chr19:49149202..49149212,-	p11@CA11
Hg19::chr19:49149234..49149251,-	p9@CA11
Hg19::chr8:107282339..107282351,+	p6@OXR1
Hg19::chr8:107440851..107440855,+	p@chr8:107440851..107440855 +
Hg19::chrX:33357425..33357435,-	p23@DMD
Hg19::chrX:33357482..33357512,-	p6@DMD
Hg19::chrX:33357525..33357536,-	p13@DMD
Hg19::chrX:33357642..33357657,-	p16@DMD

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:0043034	costamere	0.0154520836096565
GO:0043043	peptide biosynthetic process	0.0154520836096565
GO:0016998	cell wall catabolic process	0.0194157566529812
GO:0010382	cell wall metabolic process	0.0194157566529812
GO:0007047	cell wall organization and biogenesis	0.0194157566529812
GO:0016010	dystrophin-associated glycoprotein complex	0.0194157566529812
GO:0045229	external encapsulating structure organization and biogenesis	0.0194157566529812
GO:0006518	peptide metabolic process	0.0216182731161402
GO:0005605	basal lamina	0.0246949599187639
GO:0008307	structural constituent of muscle	0.0246949599187639
GO:0004089	carbonate dehydratase activity	0.0246949599187639
GO:0030016	myofibril	0.0272601251068618
GO:0044449	contractile fiber part	0.0282061916009638
GO:0043292	contractile fiber	0.0282061916009638
GO:0005604	basement membrane	0.0304302166801092
GO:0005200	structural constituent of cytoskeleton	0.0326402487061384
GO:0016836	hydro-lyase activity	0.0326402487061384
GO:0016835	carbon-oxygen lyase activity	0.0345834233518151
GO:0006979	response to oxidative stress	0.0389048363651696
GO:0044420	extracellular matrix part	0.040334478647165
GO:0006730	one-carbon compound metabolic process	0.0440785620807245
GO:0003012	muscle system process	0.0440785620807245
GO:0006936	muscle contraction	0.0440785620807245
GO:0007517	muscle development	0.0440785620807245

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	7.31e-84	56
neural rod	7.31e-84	56
future spinal cord	7.31e-84	56
neural keel	7.31e-84	56
regional part of nervous system	2.56e-76	53
regional part of brain	2.56e-76	53
central nervous system	3.16e-69	81
regional part of forebrain	1.44e-66	41
forebrain	1.44e-66	41
anterior neural tube	1.44e-66	41
future forebrain	1.44e-66	41
brain	5.95e-63	68
future brain	5.95e-63	68
brain grey matter	1.23e-61	34
gray matter	1.23e-61	34
telencephalon	1.85e-61	34
nervous system	3.09e-61	89
neural plate	8.64e-57	82
presumptive neural plate	8.64e-57	82
cerebral hemisphere	1.39e-56	32
regional part of telencephalon	2.28e-56	32
adult organism	1.05e-53	114
neurectoderm	1.22e-53	86
regional part of cerebral cortex	2.40e-49	22
pre-chordal neural plate	5.96e-45	61
neocortex	1.23e-43	20
cerebral cortex	5.59e-43	25
pallium	5.59e-43	25
ecto-epithelium	1.89e-42	104
structure with developmental contribution from neural crest	2.11e-36	132
ectoderm-derived structure	5.36e-28	171
ectoderm	5.36e-28	171
presumptive ectoderm	5.36e-28	171
organ system subdivision	4.44e-23	223
tube	3.06e-21	192
basal ganglion	3.04e-20	9
nuclear complex of neuraxis	3.04e-20	9
aggregate regional part of brain	3.04e-20	9
collection of basal ganglia	3.04e-20	9
cerebral subcortex	3.04e-20	9
neural nucleus	7.05e-20	9
nucleus of brain	7.05e-20	9
gyrus	1.06e-18	6
posterior neural tube	8.79e-18	15
chordal neural plate	8.79e-18	15
limbic system	6.54e-16	5
temporal lobe	9.53e-16	6
anatomical conduit	1.41e-15	240
telencephalic nucleus	1.09e-14	7
epithelium	1.22e-12	306
cell layer	2.12e-12	309
corpus striatum	2.79e-12	4
striatum	2.79e-12	4
ventral part of telencephalon	2.79e-12	4
future corpus striatum	2.79e-12	4
anatomical cluster	3.37e-12	373
brainstem	3.82e-12	6
segmental subdivision of hindbrain	2.42e-11	12
hindbrain	2.42e-11	12
presumptive hindbrain	2.42e-11	12
segmental subdivision of nervous system	2.20e-10	13
frontal cortex	2.46e-10	3
parietal lobe	2.80e-10	5
organ part	5.85e-10	218
occipital lobe	8.00e-10	5
caudate-putamen	1.52e-09	3
dorsal striatum	1.52e-09	3
pons	1.57e-09	3
multi-tissue structure	2.55e-09	342
spinal cord	3.13e-09	3
dorsal region element	3.13e-09	3
dorsum	3.13e-09	3
regional part of metencephalon	3.08e-08	9
metencephalon	3.08e-08	9
future metencephalon	3.08e-08	9
regional part of diencephalon	1.20e-07	4
middle temporal gyrus	1.29e-07	2
pineal body	1.41e-07	2
regional part of epithalamus	1.41e-07	2
secretory circumventricular organ	1.41e-07	2
circumventricular organ	1.41e-07	2
epithalamus	1.41e-07	2
Ammon's horn	1.93e-07	2
lobe parts of cerebral cortex	1.93e-07	2
hippocampal formation	1.93e-07	2
limbic lobe	1.93e-07	2
amygdala	2.05e-07	2
middle frontal gyrus	2.18e-07	2
diencephalon	3.34e-07	7
future diencephalon	3.34e-07	7
locus ceruleus	5.56e-07	2
brainstem nucleus	5.56e-07	2
hindbrain nucleus	5.56e-07	2
meninx	7.25e-07	2
membrane organ	7.25e-07	2
meningeal cluster	7.25e-07	2
caudate nucleus	7.92e-07	2
future caudate nucleus	7.92e-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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CTCF#10664	5	3.35016023317189	0.00764385314602122	0.0314905281336953

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.