Coexpression cluster:C472

Full id: C472_amygdala_medial_hippocampus_insula_frontal_temporal_paracentral

Phase1 CAGE Peaks

Hg19::chr10:103946143..103946171,+	p@chr10:103946143..103946171 +
Hg19::chr10:117026289..117026299,+	p@chr10:117026289..117026299 +
Hg19::chr11:64059464..64059475,+	p5@KCNK4
Hg19::chr11:99941186..99941205,+	p5@CNTN5
Hg19::chr14:76241802..76241811,+	p@chr14:76241802..76241811 +
Hg19::chr17:74864215..74864221,+	p9@MGAT5B
Hg19::chr19:54409564..54409575,+	p@chr19:54409564..54409575 +
Hg19::chr19:55690675..55690695,-	p5@SYT5
Hg19::chr19:7982540..7982547,+	p@chr19:7982540..7982547 +
Hg19::chr20:54579338..54579354,-	p3@CBLN4
Hg19::chr21:22881212..22881223,+	p@chr21:22881212..22881223 +
Hg19::chr2:242815160..242815176,+	p@chr2:242815160..242815176 +
Hg19::chr2:80816155..80816168,+	p9@CTNNA2
Hg19::chr5:146257643..146257659,-	p19@PPP2R2B
Hg19::chr5:72509751..72509785,+	p1@ENST00000513379 p1@ENST00000515556
Hg19::chr6:130742231..130742252,+	p15@TMEM200A
Hg19::chr7:130151475..130151483,+	p@chr7:130151475..130151483 +
Hg19::chr8:117658838..117658848,-	p@chr8:117658838..117658848 -
Hg19::chr9:88058857..88058883,-	p@chr9:88058857..88058883 -
Hg19::chrX:12083655..12083665,+	p@chrX:12083655..12083665 +

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:0030054	cell junction	0.00734677943850633
GO:0030144	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity	0.022457689244041
GO:0055038	recycling endosome membrane	0.0448995149596783
GO:0055037	recycling endosome	0.0458063293216049
GO:0045296	cadherin binding	0.0458063293216049
GO:0050839	cell adhesion molecule binding	0.0458063293216049
GO:0016020	membrane	0.0458063293216049

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
telencephalon	2.78e-100	34
cerebral hemisphere	1.36e-97	32
regional part of cerebral cortex	1.93e-94	22
regional part of telencephalon	1.53e-88	32
brain grey matter	2.89e-83	34
gray matter	2.89e-83	34
cerebral cortex	3.68e-83	25
pallium	3.68e-83	25
regional part of forebrain	6.66e-83	41
forebrain	6.66e-83	41
anterior neural tube	6.66e-83	41
future forebrain	6.66e-83	41
neocortex	7.12e-82	20
regional part of nervous system	2.55e-69	53
regional part of brain	2.55e-69	53
neural tube	1.88e-65	56
neural rod	1.88e-65	56
future spinal cord	1.88e-65	56
neural keel	1.88e-65	56
brain	2.44e-62	68
future brain	2.44e-62	68
central nervous system	2.78e-56	81
pre-chordal neural plate	7.53e-55	61
nervous system	2.40e-50	89
neural plate	1.24e-43	82
presumptive neural plate	1.24e-43	82
gyrus	1.66e-41	6
neurectoderm	1.97e-41	86
adult organism	7.70e-40	114
limbic system	4.45e-35	5
ecto-epithelium	1.35e-33	104
structure with developmental contribution from neural crest	4.19e-28	132
temporal lobe	1.97e-25	6
ectoderm-derived structure	1.70e-24	171
ectoderm	1.70e-24	171
presumptive ectoderm	1.70e-24	171
parietal lobe	2.50e-22	5
frontal cortex	8.23e-22	3
organ system subdivision	2.30e-19	223
basal ganglion	3.21e-19	9
nuclear complex of neuraxis	3.21e-19	9
aggregate regional part of brain	3.21e-19	9
collection of basal ganglia	3.21e-19	9
cerebral subcortex	3.21e-19	9
tube	2.79e-16	192
corpus striatum	7.44e-16	4
striatum	7.44e-16	4
ventral part of telencephalon	7.44e-16	4
future corpus striatum	7.44e-16	4
amygdala	1.54e-15	2
middle temporal gyrus	4.80e-15	2
middle frontal gyrus	6.35e-15	2
Ammon's horn	1.04e-14	2
lobe parts of cerebral cortex	1.04e-14	2
hippocampal formation	1.04e-14	2
limbic lobe	1.04e-14	2
occipital lobe	8.48e-13	5
organ part	1.79e-12	218
anatomical conduit	3.80e-12	240
caudate-putamen	7.81e-10	3
dorsal striatum	7.81e-10	3
anatomical cluster	9.62e-10	373
telencephalic nucleus	2.74e-09	7
insula	1.13e-08	1
paracentral gyrus	1.41e-08	1
epithelium	1.46e-08	306
cell layer	1.96e-08	309
olfactory region	2.02e-08	1
primary subdivision of skull	2.02e-08	1
cranium	2.02e-08	1
neurocranium	2.02e-08	1
chondrocranium	2.02e-08	1
cartilaginous neurocranium	2.02e-08	1
head paraxial mesoderm	2.02e-08	1
nucleus accumbens	2.17e-08	1
ventral striatum	2.17e-08	1
postcentral gyrus	2.89e-08	1
occipital pole	3.57e-08	1
pole of cerebral hemisphere	3.57e-08	1
multi-tissue structure	4.71e-08	342
putamen	5.82e-08	1
corpus callosum	7.16e-08	1
central nervous system cell part cluster	7.16e-08	1
axon tract	7.16e-08	1
intercerebral commissure	7.16e-08	1
dorsal telencephalic commissure	7.16e-08	1
brain white matter	7.16e-08	1
brain commissure	7.16e-08	1
white matter	7.16e-08	1
nervous system commissure	7.16e-08	1
cerebral hemisphere white matter	7.16e-08	1
neural nucleus	2.50e-07	9
nucleus of brain	2.50e-07	9

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.