Coexpression cluster:C993

Full id: C993_locus_medulla_spinal_pons_small_cerebellum_amygdala

Phase1 CAGE Peaks

Hg19::chr11:20621148..20621166,+	p1@SLC6A5
Hg19::chr11:20621167..20621170,+	p6@SLC6A5
Hg19::chr5:151304337..151304405,-	p1@GLRA1
Hg19::chr5:151304407..151304416,-	p2@GLRA1
Hg19::chr5:151304948..151304984,-	p@chr5:151304948..151304984 -
Hg19::chr5:151304987..151304998,-	p@chr5:151304987..151304998 -
Hg19::chrX:2502363..2502375,-	p@chrX:2502363..2502375 -
Hg19::chrX:2502646..2502657,-	p@chrX:2502646..2502657 -

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:0060081	membrane hyperpolarization	0.00135405628164371
GO:0002087	neurological control of breathing	0.00135405628164371
GO:0060004	reflex	0.00135405628164371
GO:0060012	synaptic transmission, glycinergic	0.00135405628164371
GO:0060013	righting reflex	0.00135405628164371
GO:0060080	regulation of inhibitory postsynaptic membrane potential	0.00135405628164371
GO:0030977	taurine binding	0.00135405628164371
GO:0007268	synaptic transmission	0.00146151165470533
GO:0019226	transmission of nerve impulse	0.00157970907739466
GO:0043576	regulation of respiratory gaseous exchange	0.00157970907739466
GO:0015375	glycine:sodium symporter activity	0.00157970907739466
GO:0003016	respiratory system process	0.00157970907739466
GO:0051970	negative regulation of transmission of nerve impulse	0.00189559509001838
GO:0005294	neutral L-amino acid secondary active transmembrane transporter activity	0.00189559509001838
GO:0016594	glycine binding	0.00189559509001838
GO:0050884	neuromuscular process controlling posture	0.00189559509001838
GO:0016934	extracellular-glycine-gated chloride channel activity	0.00189559509001838
GO:0015187	glycine transmembrane transporter activity	0.00189559509001838
GO:0060078	regulation of postsynaptic membrane potential	0.00189559509001838
GO:0001964	startle response	0.00189559509001838
GO:0016933	extracellular-glycine-gated ion channel activity	0.00215405362339861
GO:0016855	racemase and epimerase activity, acting on amino acids and derivatives	0.00215405362339861
GO:0007267	cell-cell signaling	0.00248055822458995
GO:0031645	negative regulation of neurological process	0.00276428743753103
GO:0007628	adult walking behavior	0.00291612843739686
GO:0051291	protein heterooligomerization	0.00291612843739686
GO:0007340	acrosome reaction	0.00315909263813393
GO:0005283	sodium:amino acid symporter activity	0.00406151116842331
GO:0017156	calcium ion-dependent exocytosis	0.00410657861720154
GO:0005416	cation:amino acid symporter activity	0.00410657861720154
GO:0008344	adult locomotory behavior	0.00427974597748268
GO:0015175	neutral amino acid transmembrane transporter activity	0.00503421098668936
GO:0051969	regulation of transmission of nerve impulse	0.00516873946372341
GO:0007270	nerve-nerve synaptic transmission	0.0052953462946297
GO:0016597	amino acid binding	0.00541471047764775
GO:0050905	neuromuscular process	0.00594927216790162
GO:0050877	neurological system process	0.00594927216790162
GO:0016854	racemase and epimerase activity	0.00594927216790162
GO:0031644	regulation of neurological process	0.00594927216790162
GO:0015075	ion transmembrane transporter activity	0.00594927216790162
GO:0005887	integral to plasma membrane	0.00594927216790162
GO:0031226	intrinsic to plasma membrane	0.00594927216790162
GO:0030534	adult behavior	0.00594927216790162
GO:0005275	amine transmembrane transporter activity	0.00610578100839108
GO:0007585	respiratory gaseous exchange	0.00610578100839108
GO:0042391	regulation of membrane potential	0.00638479285822445
GO:0022891	substrate-specific transmembrane transporter activity	0.00686232643694342
GO:0003008	system process	0.00687939342854417
GO:0005343	organic acid:sodium symporter activity	0.00728688707163315
GO:0004890	GABA-A receptor activity	0.00728688707163315
GO:0022857	transmembrane transporter activity	0.00728688707163315
GO:0001508	regulation of action potential	0.00728688707163315
GO:0051260	protein homooligomerization	0.00732802568161109
GO:0043176	amine binding	0.00771824791187268
GO:0022892	substrate-specific transporter activity	0.00790622462079804
GO:0016917	GABA receptor activity	0.00794969468264957
GO:0005328	neurotransmitter:sodium symporter activity	0.00816513631184729
GO:0009897	external side of plasma membrane	0.00816513631184729
GO:0005326	neurotransmitter transporter activity	0.00850797286131233
GO:0007338	single fertilization	0.00883933967365377
GO:0009566	fertilization	0.0090046826188368
GO:0031404	chloride ion binding	0.00901920290510728
GO:0043168	anion binding	0.00901920290510728
GO:0051259	protein oligomerization	0.0091739501599589
GO:0015171	amino acid transmembrane transporter activity	0.00917836777421169
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0103292606887706
GO:0044459	plasma membrane part	0.0108599536750957
GO:0006836	neurotransmitter transport	0.0108599536750957
GO:0005254	chloride channel activity	0.0112507492645326
GO:0006821	chloride transport	0.0117328253921666
GO:0015370	solute:sodium symporter activity	0.0117328253921666
GO:0046943	carboxylic acid transmembrane transporter activity	0.0127514600662058
GO:0005342	organic acid transmembrane transporter activity	0.0127899767092456
GO:0005253	anion channel activity	0.0127899767092456
GO:0006887	exocytosis	0.0140053113157588
GO:0015294	solute:cation symporter activity	0.0141939444973642
GO:0005230	extracellular ligand-gated ion channel activity	0.0160947247234644
GO:0030594	neurotransmitter receptor activity	0.0170987138343306
GO:0042165	neurotransmitter binding	0.0173601799598286
GO:0009986	cell surface	0.017397583831441
GO:0045211	postsynaptic membrane	0.017397583831441
GO:0044456	synapse part	0.0181413946760884
GO:0015276	ligand-gated ion channel activity	0.0181413946760884
GO:0022834	ligand-gated channel activity	0.0181413946760884
GO:0003012	muscle system process	0.0181413946760884
GO:0006936	muscle contraction	0.0181413946760884
GO:0007218	neuropeptide signaling pathway	0.0182581169534328
GO:0007626	locomotory behavior	0.0194436837077933
GO:0008509	anion transmembrane transporter activity	0.0221901088285466
GO:0005886	plasma membrane	0.0223883845240826
GO:0032501	multicellular organismal process	0.0223883845240826
GO:0007601	visual perception	0.0226534990889344
GO:0050953	sensory perception of light stimulus	0.0226534990889344
GO:0055082	cellular chemical homeostasis	0.0233228061816399
GO:0006873	cellular ion homeostasis	0.0233228061816399
GO:0045045	secretory pathway	0.0233228061816399
GO:0006810	transport	0.0233228061816399
GO:0015293	symporter activity	0.0233228061816399
GO:0051234	establishment of localization	0.024088359323175
GO:0015698	inorganic anion transport	0.0245498802191714
GO:0050801	ion homeostasis	0.024958644697381
GO:0051239	regulation of multicellular organismal process	0.0256357797097164
GO:0007610	behavior	0.0266935110287568
GO:0051179	localization	0.0266935110287568
GO:0032940	secretion by cell	0.0266935110287568
GO:0048878	chemical homeostasis	0.0268848443540973
GO:0022414	reproductive process	0.0268969631726346
GO:0016853	isomerase activity	0.0272650958715835
GO:0019953	sexual reproduction	0.0272650958715835
GO:0006820	anion transport	0.0277001061218117
GO:0006461	protein complex assembly	0.0288880572755278
GO:0015291	secondary active transmembrane transporter activity	0.0303052850645014
GO:0019725	cellular homeostasis	0.0312816979044878
GO:0046903	secretion	0.0317472429057463
GO:0030054	cell junction	0.0351357898186916
GO:0007154	cell communication	0.0371714845023831
GO:0042592	homeostatic process	0.0386115694457162
GO:0022836	gated channel activity	0.0402634033800093
GO:0016192	vesicle-mediated transport	0.0478383129808364
GO:0009605	response to external stimulus	0.0495334393029555

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>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
embryonic stem cell	2.73e-12	5

Uber Anatomy

Ontology term	p-value	n
neural tube	1.57e-74	57
neural rod	1.57e-74	57
future spinal cord	1.57e-74	57
neural keel	1.57e-74	57
central nervous system	1.87e-65	82
regional part of nervous system	1.45e-64	94
nervous system	1.45e-64	94
regional part of brain	9.34e-61	59
brain	7.99e-58	69
future brain	7.99e-58	69
regional part of forebrain	1.46e-52	41
forebrain	1.46e-52	41
future forebrain	1.46e-52	41
neural plate	2.90e-52	86
presumptive neural plate	2.90e-52	86
neurectoderm	8.77e-52	90
anterior neural tube	4.17e-51	42
gray matter	2.61e-43	34
brain grey matter	2.61e-43	34
telencephalon	1.41e-42	34
adult organism	1.80e-41	115
regional part of telencephalon	1.40e-40	33
cerebral hemisphere	5.32e-39	32
pre-chordal neural plate	7.77e-35	61
regional part of cerebral cortex	3.20e-33	22
neocortex	5.20e-33	20
ectoderm	9.12e-33	173
presumptive ectoderm	9.12e-33	173
ectoderm-derived structure	2.12e-32	169
head	2.08e-30	123
anterior region of body	8.35e-30	129
craniocervical region	8.35e-30	129
cerebral cortex	9.67e-29	25
pallium	9.67e-29	25
posterior neural tube	9.80e-24	15
chordal neural plate	9.80e-24	15
tube	1.07e-19	194
segmental subdivision of hindbrain	6.88e-17	12
hindbrain	6.88e-17	12
presumptive hindbrain	6.88e-17	12
nucleus of brain	3.01e-16	9
neural nucleus	3.01e-16	9
basal ganglion	4.53e-16	9
nuclear complex of neuraxis	4.53e-16	9
aggregate regional part of brain	4.53e-16	9
collection of basal ganglia	4.53e-16	9
cerebral subcortex	4.53e-16	9
brainstem	1.48e-15	8
segmental subdivision of nervous system	2.01e-15	13
gyrus	1.19e-14	6
temporal lobe	3.08e-14	7
anatomical conduit	3.15e-13	241
parietal lobe	2.26e-12	5
telencephalic nucleus	1.38e-11	7
diencephalon	3.19e-11	7
future diencephalon	3.19e-11	7
anatomical cluster	5.36e-11	286
regional part of metencephalon	2.48e-10	9
metencephalon	2.48e-10	9
future metencephalon	2.48e-10	9
organ part	4.48e-10	219
epithelium	7.87e-10	309
cell layer	1.32e-09	312
organism subdivision	1.73e-09	365
medulla oblongata	5.64e-09	3
myelencephalon	5.64e-09	3
future myelencephalon	5.64e-09	3
pons	5.94e-09	3
spinal cord	5.94e-09	3
middle temporal gyrus	2.39e-08	3
brainstem nucleus	2.63e-08	3
limbic system	4.19e-08	5
embryo	3.26e-07	612

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
REST#5978	4	4.82501435806401	0.00572073539826954	0.0257896095420155

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.