Coexpression cluster:C494

Full id: C494_occipital_medial_brain_Whole_caudate_parietal_blood

Phase1 CAGE Peaks

Hg19::chr11:124615395..124615405,+	p@chr11:124615395..124615405 +
Hg19::chr11:124615417..124615426,+	p@chr11:124615417..124615426 +
Hg19::chr11:124615444..124615454,+	p@chr11:124615444..124615454 +
Hg19::chr11:124615466..124615503,+	p@chr11:124615466..124615503 +
Hg19::chr11:124615584..124615600,+	p@chr11:124615584..124615600 +
Hg19::chr11:124616294..124616374,+	p@chr11:124616294..124616374 +
Hg19::chr11:124616375..124616422,+	p@chr11:124616375..124616422 +
Hg19::chr11:124616427..124616476,+	p@chr11:124616427..124616476 +
Hg19::chr11:124616482..124616540,+	p@chr11:124616482..124616540 +
Hg19::chr11:124616552..124616569,+	p@chr11:124616552..124616569 +
Hg19::chr11:124616611..124616623,+	p@chr11:124616611..124616623 +
Hg19::chr11:124616640..124616647,+	p@chr11:124616640..124616647 +
Hg19::chr11:124616709..124616718,+	p@chr11:124616709..124616718 +
Hg19::chr11:35275624..35275635,-	p14@SLC1A2
Hg19::chr11:35277083..35277090,-	p47@SLC1A2
Hg19::chr12:49389153..49389154,-	p@chr12:49389153..49389154 -
Hg19::chr16:743961..743974,-	p@chr16:743961..743974 -
Hg19::chr2:68479697..68479708,-	p2@PPP3R1
Hg19::chr8:21939098..21939104,+	p@chr8:21939098..21939104 +

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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p.value	FDR	nGenes	nPathway	Name
1.93288158883898e-05	0.00611757022867537	2	126	Glutamatergic synapse (KEGG):04724
3.38223597386681e-06	0.00214095537145769	2	53	Amyotrophic lateral sclerosis (ALS) (KEGG):05014

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:0005517	calmodulin inhibitor activity	0.00382662447319203
GO:0004723	calcium-dependent protein serine/threonine phosphatase activity	0.00382662447319203
GO:0005955	calcineurin complex	0.0051020157702358
GO:0005313	L-glutamate transmembrane transporter activity	0.00650382537410799
GO:0015172	acidic amino acid transmembrane transporter activity	0.00650382537410799
GO:0015813	L-glutamate transport	0.00650382537410799
GO:0015800	acidic amino acid transport	0.00650382537410799
GO:0017153	sodium:dicarboxylate symporter activity	0.00650382537410799
GO:0005310	dicarboxylic acid transmembrane transporter activity	0.00650382537410799
GO:0006835	dicarboxylic acid transport	0.00650382537410799
GO:0015179	L-amino acid transmembrane transporter activity	0.0111270830268056
GO:0005343	organic acid:sodium symporter activity	0.011473621593484
GO:0015296	anion:cation symporter activity	0.011473621593484
GO:0008287	protein serine/threonine phosphatase complex	0.0155312468165728
GO:0015171	amino acid transmembrane transporter activity	0.0155312468165728
GO:0004722	protein serine/threonine phosphatase activity	0.0155312468165728
GO:0006865	amino acid transport	0.0157409186351371
GO:0015837	amine transport	0.0164476067567351
GO:0015370	solute:sodium symporter activity	0.0164476067567351
GO:0046943	carboxylic acid transmembrane transporter activity	0.0164476067567351
GO:0046942	carboxylic acid transport	0.0164476067567351
GO:0015849	organic acid transport	0.0164476067567351
GO:0005342	organic acid transmembrane transporter activity	0.0164476067567351
GO:0015294	solute:cation symporter activity	0.018146502540626
GO:0005516	calmodulin binding	0.0215380072397654
GO:0008509	anion transmembrane transporter activity	0.0306664547475256
GO:0015293	symporter activity	0.0341767369167349
GO:0007268	synaptic transmission	0.0394648935897162
GO:0004721	phosphoprotein phosphatase activity	0.0411120977212879
GO:0019226	transmission of nerve impulse	0.0418896566957398
GO:0015291	secondary active transmembrane transporter activity	0.0442040623661732

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	1.56e-62	34
cerebral hemisphere	2.84e-62	32
regional part of forebrain	8.35e-59	41
forebrain	8.35e-59	41
anterior neural tube	8.35e-59	41
future forebrain	8.35e-59	41
brain grey matter	6.81e-58	34
gray matter	6.81e-58	34
regional part of telencephalon	1.84e-57	32
regional part of nervous system	3.96e-50	53
regional part of brain	3.96e-50	53
regional part of cerebral cortex	5.13e-50	22
neural tube	5.14e-47	56
neural rod	5.14e-47	56
future spinal cord	5.14e-47	56
neural keel	5.14e-47	56
neocortex	1.07e-44	20
adult organism	7.26e-44	114
cerebral cortex	1.39e-43	25
pallium	1.39e-43	25
brain	2.95e-42	68
future brain	2.95e-42	68
central nervous system	7.62e-39	81
pre-chordal neural plate	4.36e-37	61
nervous system	4.44e-34	89
neurectoderm	1.19e-29	86
neural plate	1.70e-29	82
presumptive neural plate	1.70e-29	82
ecto-epithelium	4.81e-23	104
basal ganglion	1.80e-20	9
nuclear complex of neuraxis	1.80e-20	9
aggregate regional part of brain	1.80e-20	9
collection of basal ganglia	1.80e-20	9
cerebral subcortex	1.80e-20	9
blood	7.66e-19	15
haemolymphatic fluid	7.66e-19	15
organism substance	7.66e-19	15
gyrus	8.66e-19	6
structure with developmental contribution from neural crest	1.15e-17	132
temporal lobe	1.36e-15	6
ectoderm-derived structure	1.54e-15	171
ectoderm	1.54e-15	171
presumptive ectoderm	1.54e-15	171
neural nucleus	1.98e-15	9
nucleus of brain	1.98e-15	9
telencephalic nucleus	3.49e-15	7
limbic system	4.10e-15	5
corpus striatum	6.90e-13	4
striatum	6.90e-13	4
ventral part of telencephalon	6.90e-13	4
future corpus striatum	6.90e-13	4
organ system subdivision	2.45e-11	223
occipital lobe	8.79e-11	5
parietal lobe	1.43e-10	5
frontal cortex	3.57e-10	3
caudate-putamen	3.80e-10	3
dorsal striatum	3.80e-10	3
tube	1.84e-09	192
middle temporal gyrus	1.97e-07	2
middle frontal gyrus	2.23e-07	2
caudate nucleus	2.30e-07	2
future caudate nucleus	2.30e-07	2
germ layer	2.73e-07	560
germ layer / neural crest	2.73e-07	560
embryonic tissue	2.73e-07	560
presumptive structure	2.73e-07	560
germ layer / neural crest derived structure	2.73e-07	560
epiblast (generic)	2.73e-07	560
embryonic structure	3.87e-07	564
amygdala	4.52e-07	2
Ammon's horn	5.76e-07	2
lobe parts of cerebral cortex	5.76e-07	2
hippocampal formation	5.76e-07	2
limbic lobe	5.76e-07	2
meninx	6.89e-07	2
membrane organ	6.89e-07	2
meningeal cluster	6.89e-07	2
hematopoietic system	8.02e-07	98
blood island	8.02e-07	98

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
CTBP2#1488	13	42.9116318111192	1.04100712274376e-19	2.58246420171582e-17
CTCF#10664	9	2.5390688082987	0.00410317010119337	0.0195908833408857
JUND#3727	7	2.57698145226827	0.0126591568064184	0.0457619908520136
RAD21#5885	7	3.8150124877997	0.00138020032943887	0.0089844641115848
SMC3#9126	7	5.54286999550157	0.000141120446354047	0.00183978008947327
SP1#6667	8	2.39931847500669	0.0107940320275902	0.0398078290522084
SPI1#6688	8	3.45445200358852	0.00105342463012797	0.00744425299045502
SUZ12#23512	3	7.91301803858888	0.006055807111597	0.0268595761212927
ZNF143#7702	7	4.97400715082081	0.000276950984269634	0.00294967202183727

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.