Coexpression cluster:C118

Full id: C118_cerebellum_parietal_occipital_medial_middle_frontal_insula

Phase1 CAGE Peaks

Hg19::chr10:105037220..105037227,+	p12@INA
Hg19::chr10:18689498..18689550,+	p6@CACNB2
Hg19::chr10:24911746..24911793,-	p6@ARHGAP21
Hg19::chr10:25463662..25463680,+	p1@GPR158
Hg19::chr10:25463691..25463702,+	p5@GPR158
Hg19::chr10:25463726..25463735,+	p6@GPR158
Hg19::chr10:62149714..62149724,-	p34@ANK3
Hg19::chr10:65281549..65281566,-	p@chr10:65281549..65281566 -
Hg19::chr11:105480715..105480735,+	p6@GRIA4
Hg19::chr11:105480793..105480845,+	p3@GRIA4
Hg19::chr11:119019778..119019795,+	p2@ABCG4
Hg19::chr11:132714823..132714843,-	p@chr11:132714823..132714843 -
Hg19::chr11:132813716..132813736,-	p14@OPCML
Hg19::chr11:17172291..17172318,-	p@chr11:17172291..17172318 -
Hg19::chr11:17756279..17756367,+	p1@KCNC1
Hg19::chr11:47616210..47616237,-	p4@C1QTNF4
Hg19::chr11:66025938..66025957,+	p9@KLC2
Hg19::chr11:66790693..66790733,+	p2@SYT12
Hg19::chr11:94134581..94134594,-	p1@GPR83
Hg19::chr12:100378459..100378530,-	p6@ANKS1B
Hg19::chr12:108523053..108523101,+	p1@WSCD2
Hg19::chr12:108525551..108525568,+	p4@WSCD2
Hg19::chr12:119419159..119419192,+	p5@SRRM4
Hg19::chr12:132904597..132904617,+	p@chr12:132904597..132904617 +
Hg19::chr12:132906118..132906180,-	p1@GALNT9
Hg19::chr12:3601977..3601990,-	p1@uc001qmd.1
Hg19::chr12:52214727..52214749,-	p@chr12:52214727..52214749 -
Hg19::chr13:103054704..103054731,-	p2@FGF14-IT1
Hg19::chr14:24047796..24047818,-	p10@JPH4
Hg19::chr14:27067258..27067276,-	p3@NOVA1
Hg19::chr15:31658288..31658338,+	p4@KLF13
Hg19::chr15:31658340..31658347,+	p34@KLF13
Hg19::chr15:37391438..37391479,+	p1@ENST00000559509
Hg19::chr15:40650463..40650527,+	p1@DISP2
Hg19::chr16:31004138..31004144,+	p@chr16:31004138..31004144 +
Hg19::chr16:330675..330686,+	p3@PDIA2 p4@ARHGDIG
Hg19::chr16:6069299..6069316,+	p18@RBFOX1
Hg19::chr16:6069333..6069361,+	p10@RBFOX1
Hg19::chr16:6069840..6069851,+	p31@RBFOX1
Hg19::chr16:87636569..87636577,+	p6@JPH3
Hg19::chr17:19314532..19314563,+	p1@RNF112
Hg19::chr17:2658922..2658963,+	p@chr17:2658922..2658963 +
Hg19::chr17:43319081..43319146,-	p1@AK096807
Hg19::chr17:48207115..48207152,-	p4@SAMD14
Hg19::chr17:50235163..50235180,-	p16@CA10
Hg19::chr17:50235879..50235899,-	p14@CA10
Hg19::chr17:50237348..50237373,-	p5@CA10
Hg19::chr17:50237374..50237388,-	p9@CA10
Hg19::chr17:72857858..72857869,-	p@chr17:72857858..72857869 -
Hg19::chr17:7452189..7452207,+	p3@TNFSF12-TNFSF13 p3@TNFSF12
Hg19::chr17:77090555..77090587,-	p@chr17:77090555..77090587 -
Hg19::chr17:79373129..79373161,+	p3@BAHCC1
Hg19::chr17:80656875..80656912,+	p@chr17:80656875..80656912 +
Hg19::chr18:3874247..3874262,-	p9@DLGAP1
Hg19::chr18:3874271..3874337,-	p3@DLGAP1
Hg19::chr18:44336896..44336907,+	p@chr18:44336896..44336907 +
Hg19::chr19:13106465..13106477,+	p27@NFIX
Hg19::chr19:13616887..13616912,-	p10@CACNA1A
Hg19::chr19:13617037..13617069,-	p4@CACNA1A
Hg19::chr19:13618233..13618292,-	p@chr19:13618233..13618292 -
Hg19::chr19:30019801..30019814,+	p@chr19:30019801..30019814 +
Hg19::chr19:3987889..3987898,-	p@chr19:3987889..3987898 -
Hg19::chr19:41036371..41036417,+	p1@SPTBN4
Hg19::chr19:42817511..42817522,+	p6@TMEM145
Hg19::chr19:42817550..42817569,+	p3@TMEM145
Hg19::chr19:44139537..44139540,+	p@chr19:44139537..44139540 +
Hg19::chr1:11714458..11714482,+	p2@FBXO44
Hg19::chr1:174768671..174768682,+	p29@RABGAP1L
Hg19::chr1:174769436..174769459,+	p15@RABGAP1L
Hg19::chr1:205414261..205414293,-	p@chr1:205414261..205414293 -
Hg19::chr1:2398876..2398928,+	p1@PLCH2
Hg19::chr1:244211767..244211800,+	p@chr1:244211767..244211800 +
Hg19::chr20:10289444..10289460,+	p@chr20:10289444..10289460 +
Hg19::chr20:3767547..3767623,+	p4@CDC25B
Hg19::chr20:3767689..3767696,+	p8@CDC25B
Hg19::chr20:44036054..44036086,-	p1@AK098015
Hg19::chr20:44937047..44937095,-	p1@CDH22
Hg19::chr20:44937096..44937105,-	p7@CDH22
Hg19::chr20:45980455..45980466,-	p24@ZMYND8
Hg19::chr20:9819653..9819663,-	p5@PAK7
Hg19::chr22:18958039..18958055,+	p2@DGCR5
Hg19::chr22:37099555..37099599,-	p2@CACNG2
Hg19::chr22:51066685..51066719,+	p@chr22:51066685..51066719 +
Hg19::chr2:100721281..100721307,-	p5@AFF3
Hg19::chr2:152830428..152830439,-	p7@CACNB4
Hg19::chr2:152830441..152830472,-	p2@CACNB4
Hg19::chr2:152830479..152830503,-	p3@CACNB4
Hg19::chr2:155553962..155553969,+	p@chr2:155553962..155553969 +
Hg19::chr2:155554040..155554063,+	p@chr2:155554040..155554063 +
Hg19::chr2:155555201..155555272,+	p1@KCNJ3
Hg19::chr2:173600040..173600056,+	p20@RAPGEF4
Hg19::chr2:17773946..17773949,+	p@chr2:17773946..17773949 +
Hg19::chr2:183387533..183387548,-	p7@PDE1A
Hg19::chr2:197457394..197457421,-	p12@HECW2
Hg19::chr2:210636313..210636335,+	p3@UNC80
Hg19::chr2:2328418..2328441,-	p13@MYT1L
Hg19::chr2:39893140..39893164,+	p8@TMEM178
Hg19::chr2:39893171..39893182,+	p13@TMEM178
Hg19::chr2:47798782..47798832,-	p@chr2:47798782..47798832 -
Hg19::chr2:50201327..50201339,-	p18@NRXN1
Hg19::chr3:113251885..113251917,+	p4@SIDT1
Hg19::chr3:120627034..120627102,+	p1@STXBP5L
Hg19::chr3:120627517..120627530,+	p2@STXBP5L
Hg19::chr3:120989095..120989099,+	p@chr3:120989095..120989099 +
Hg19::chr3:132843652..132843709,+	p3@TMEM108
Hg19::chr3:138153411..138153433,+	p2@ESYT3
Hg19::chr3:173113898..173113949,+	p4@NLGN1
Hg19::chr3:182833946..182833990,-	p5@MCCC1
Hg19::chr3:184098065..184098119,+	p1@CHRD
Hg19::chr3:186080012..186080030,-	p1@DGKG
Hg19::chr3:186080056..186080061,-	p5@DGKG
Hg19::chr3:35722538..35722559,+	p27@ARPP21
Hg19::chr3:37903001..37903039,+	p6@CTDSPL
Hg19::chr3:52489503..52489540,+	p2@NISCH
Hg19::chr3:96532248..96532290,+	p@chr3:96532248..96532290 +
Hg19::chr4:103998320..103998345,-	p10@SLC9B2
Hg19::chr4:114038052..114038059,+	p34@ANK2
Hg19::chr4:118955635..118955655,+	p3@NDST3
Hg19::chr5:110559790..110559803,+	p11@CAMK4
Hg19::chr5:110559929..110559940,+	p8@CAMK4
Hg19::chr5:110559941..110559952,+	p4@CAMK4
Hg19::chr5:138211051..138211072,-	p3@LRRTM2
Hg19::chr5:156772748..156772774,-	p3@FNDC9
Hg19::chr5:160975364..160975379,-	p5@GABRB2
Hg19::chr5:19873309..19873311,-	p@chr5:19873309..19873311 -
Hg19::chr5:19988288..19988330,-	p1@CDH18
Hg19::chr5:41510865..41510886,-	p4@PLCXD3
Hg19::chr5:87981322..87981337,-	p@chr5:87981322..87981337 -
Hg19::chr5:94620239..94620258,-	p6@MCTP1
Hg19::chr6:101846679..101846702,+	p1@GRIK2
Hg19::chr6:101846725..101846734,+	p17@GRIK2
Hg19::chr6:69345285..69345308,+	p2@BAI3
Hg19::chr6:69345833..69345845,+	p8@BAI3
Hg19::chr6:72596229..72596272,+	p2@RIMS1
Hg19::chr6:72596410..72596454,+	p4@RIMS1
Hg19::chr6:72596604..72596697,+	p1@RIMS1
Hg19::chr7:151511911..151511962,-	p9@PRKAG2
Hg19::chr7:28997721..28997738,-	p3@TRIL
Hg19::chr7:71801984..71802013,-	p3@CALN1
Hg19::chr8:10158687..10158707,+	p4@MSRA
Hg19::chr8:132928997..132929025,+	p@chr8:132928997..132929025 +
Hg19::chr8:15095883..15095918,-	p1@SGCZ
Hg19::chr8:15095933..15095945,-	p3@SGCZ
Hg19::chr8:85095907..85095910,+	p5@RALYL
Hg19::chr8:9761882..9761897,-	p3@ENST00000521863
Hg19::chr8:9776628..9776670,-	p@chr8:9776628..9776670 -
Hg19::chr8:9911618..9911629,+	p8@MSRA
Hg19::chr8:9953920..9953944,+	p@chr8:9953920..9953944 +
Hg19::chr9:100264031..100264042,+	p4@TMOD1
Hg19::chr9:15250159..15250231,-	p2@TTC39B
Hg19::chr9:79307096..79307129,-	p2@PRUNE2
Hg19::chrX:123510693..123510711,-	p1@ODZ1
Hg19::chrX:21392356..21392365,+	p7@CNKSR2

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
3.21588558482119e-05	0.00678551858397271	5	126	Glutamatergic synapse (KEGG):04724
9.77861502511732e-05	0.0123824018731482	4	83	Hypertrophic cardiomyopathy (HCM) (KEGG):05410
0.000106696491900211	0.0123824018731482	3	32	Hypothetical Network for Drug Addiction (Wikipathways):WP666
2.70775915789819e-10	1.71401154694955e-07	10	197	Synaptic Transmission (Reactome):REACT_13685
0.000470699126992762	0.0425646496266312	4	125	Integration of energy metabolism (Reactome):REACT_1505
0.000117368738134106	0.0123824018731482	6	265	Axon guidance (Reactome):REACT_18266
9.00885823625835e-07	0.000285130363177577	4	26	{RASGRF1,26} (Static Module):NA

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:0005886	plasma membrane	2.52069622669271e-06
GO:0030054	cell junction	1.17290317297813e-05
GO:0044425	membrane part	1.73607675976265e-05
GO:0044459	plasma membrane part	1.96924833961766e-05
GO:0016021	integral to membrane	2.96607884633392e-05
GO:0031224	intrinsic to membrane	2.96607884633392e-05
GO:0016020	membrane	2.96607884633392e-05
GO:0019226	transmission of nerve impulse	5.52398222233686e-05
GO:0005891	voltage-gated calcium channel complex	9.62884579184354e-05
GO:0044456	synapse part	0.000100003913961408
GO:0022836	gated channel activity	0.000100003913961408
GO:0007268	synaptic transmission	0.000195909142086055
GO:0005245	voltage-gated calcium channel activity	0.000735829937860229
GO:0005216	ion channel activity	0.000774514386210364
GO:0045211	postsynaptic membrane	0.000774514386210364
GO:0022838	substrate specific channel activity	0.000774514386210364
GO:0022843	voltage-gated cation channel activity	0.000774514386210364
GO:0022803	passive transmembrane transporter activity	0.000774514386210364
GO:0015267	channel activity	0.000774514386210364
GO:0005509	calcium ion binding	0.00232511436195309
GO:0022832	voltage-gated channel activity	0.00232511436195309
GO:0005244	voltage-gated ion channel activity	0.00232511436195309
GO:0007267	cell-cell signaling	0.00232511436195309
GO:0050808	synapse organization and biogenesis	0.00235257978902726
GO:0016079	synaptic vesicle exocytosis	0.00325202505564878
GO:0007154	cell communication	0.00325202505564878
GO:0005262	calcium channel activity	0.00336573353867295
GO:0007528	neuromuscular junction development	0.00483663614046024
GO:0005261	cation channel activity	0.00737641660664985
GO:0048489	synaptic vesicle transport	0.015006921745046
GO:0006816	calcium ion transport	0.015006921745046
GO:0046873	metal ion transmembrane transporter activity	0.0164919554253955
GO:0043062	extracellular structure organization and biogenesis	0.0166120175719292
GO:0005200	structural constituent of cytoskeleton	0.0166869234776399
GO:0006790	sulfur metabolic process	0.0166902838132157
GO:0005515	protein binding	0.0166902838132157
GO:0007215	glutamate signaling pathway	0.0168140216446291
GO:0044464	cell part	0.0192693977562345
GO:0008066	glutamate receptor activity	0.0194643442025702
GO:0006887	exocytosis	0.0305731989543396
GO:0006810	transport	0.0318329478143315
GO:0048172	regulation of short-term neuronal synaptic plasticity	0.0318329478143315
GO:0031557	induction of programmed cell death in response to chemical stimulus	0.0318329478143315
GO:0015674	di-, tri-valent inorganic cation transport	0.0318329478143315
GO:0015075	ion transmembrane transporter activity	0.0348655253979806
GO:0004970	ionotropic glutamate receptor activity	0.0399196833593958
GO:0006811	ion transport	0.0399196833593958
GO:0051234	establishment of localization	0.0399196833593958
GO:0005230	extracellular ligand-gated ion channel activity	0.0399196833593958
GO:0051179	localization	0.0414994901283276
GO:0005234	extracellular-glutamate-gated ion channel activity	0.0419511124508003
GO:0007269	neurotransmitter secretion	0.042722762846028
GO:0008081	phosphoric diester hydrolase activity	0.042722762846028
GO:0048741	skeletal muscle fiber development	0.0443533759491619
GO:0048747	muscle fiber development	0.0443533759491619
GO:0005856	cytoskeleton	0.0443533759491619
GO:0030001	metal ion transport	0.0443533759491619
GO:0006552	leucine catabolic process	0.0457689282451179
GO:0006768	biotin metabolic process	0.0457689282451179
GO:0016080	synaptic vesicle targeting	0.0457689282451179
GO:0004485	methylcrotonoyl-CoA carboxylase activity	0.0457689282451179

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
neural cell	4.40e-07	25

Uber Anatomy

Ontology term	p-value	n
adult organism	1.25e-48	115
regional part of nervous system	1.53e-39	94
nervous system	1.53e-39	94
central nervous system	7.00e-38	82
neural tube	3.67e-34	57
neural rod	3.67e-34	57
future spinal cord	3.67e-34	57
neural keel	3.67e-34	57
neurectoderm	7.81e-32	90
neural plate	3.05e-31	86
presumptive neural plate	3.05e-31	86
brain	5.61e-31	69
future brain	5.61e-31	69
regional part of brain	3.91e-29	59
anterior neural tube	3.26e-26	42
regional part of forebrain	5.94e-26	41
forebrain	5.94e-26	41
future forebrain	5.94e-26	41
ectoderm	2.97e-24	173
presumptive ectoderm	2.97e-24	173
ectoderm-derived structure	1.77e-23	169
telencephalon	6.34e-22	34
gray matter	6.55e-22	34
brain grey matter	6.55e-22	34
pre-chordal neural plate	2.10e-21	61
regional part of telencephalon	2.89e-21	33
cerebral hemisphere	7.92e-21	32
anterior region of body	9.33e-20	129
craniocervical region	9.33e-20	129
head	5.17e-19	123
cerebral cortex	1.50e-16	25
pallium	1.50e-16	25
regional part of cerebral cortex	5.37e-16	22
neocortex	8.69e-15	20
organism subdivision	2.96e-09	365
posterior neural tube	5.26e-09	15
chordal neural plate	5.26e-09	15
tube	3.88e-08	194
multi-cellular organism	4.32e-08	659
segmental subdivision of nervous system	7.10e-08	13
segmental subdivision of hindbrain	2.32e-07	12
hindbrain	2.32e-07	12
presumptive hindbrain	2.32e-07	12
basal ganglion	7.02e-07	9
nuclear complex of neuraxis	7.02e-07	9
aggregate regional part of brain	7.02e-07	9
collection of basal ganglia	7.02e-07	9
cerebral subcortex	7.02e-07	9
nucleus of brain	8.21e-07	9
neural nucleus	8.21e-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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CTBP2#1488	12	4.91898041877083	7.36337494877413e-06	0.000211386343121226
CTCF#10664	45	1.57654599208089	0.000837623142862051	0.00631902076115066
RAD21#5885	33	2.23343868333372	8.74177219459004e-06	0.00023597362270116
SUZ12#23512	10	3.27554123601718	0.00107559596656458	0.00759579195023588
ZNF263#10127	32	1.71960086525714	0.00148467697309175	0.00949529567622349

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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