SZGR2

Summary ?

GeneID	7416
Symbol	VDAC1
Synonyms	PORIN\|VDAC-1
Description	voltage dependent anion channel 1
Reference	MIM:604492\|HGNC:HGNC:12669\|Ensembl:ENSG00000213585\|HPRD:05137\|Vega:OTTHUMG00000129118
Gene type	protein-coding
Map location	5q31
Pascal p-value	0.838
Sherlock p-value	0.002
Fetal beta	-1.176
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	EXCITABILITY G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.human_clathrin G2Cdb.human_mitochondria G2Cdb.human_Synaptosome G2Cdb.human_TAP-PSD-95-CORE G2Cdb.humanNRC G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	1
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_I	Genome scan meta-analysis	Psr: 0.0032
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias	Click to show details
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.131

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
VDAC1	chr5	133326732	G	A	NM_003374 NR_036624 NR_036625	. . .	silent npcRNA npcRNA			Schizophrenia	DNM:Fromer_2014

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg15094104	5	133406808	VDAC1	2.76E-8	-0.025	8.68E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs10994209	chr10	61877705	VDAC1	7416		0.11		trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IPI		17353931
GO:0008308	voltage-gated anion channel activity	TAS		8420959
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006820	anion transport	TAS		8420959
GO:0008632	apoptotic program	TAS		10365962
GO:0044419	interspecies interaction between organisms	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005739	mitochondrion	TAS		8420959
GO:0005741	mitochondrial outer membrane	TAS		8420959
GO:0005886	plasma membrane	IEA		-
GO:0046930	pore complex	TAS		9843949

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
BAX	BCL2L4	BCL2-associated X protein	-	HPRD	9843949 \|12767928\|12767928
BAX	BCL2L4	BCL2-associated X protein	-	HPRD,BioGRID	12767928
BCL2L1	BCL-XL/S \| BCL2L \| BCLX \| Bcl-X \| DKFZp781P2092 \| bcl-xL \| bcl-xS	BCL2-like 1	Affinity Capture-Western Reconstituted Complex	BioGRID	10365962 \|10737788 \|12767928 \|15637055
BCL2L1	BCL-XL/S \| BCL2L \| BCLX \| Bcl-X \| DKFZp781P2092 \| bcl-xL \| bcl-xS	BCL2-like 1	-	HPRD	10049775 \|10365962 \|10737788
BCL2L11	BAM \| BIM \| BIM-alpha6 \| BIM-beta6 \| BIM-beta7 \| BOD \| BimEL \| BimL	BCL2-like 11 (apoptosis facilitator)	-	HPRD,BioGRID	12118373
CKMT1B	CKMT \| CKMT1 \| UMTCK	creatine kinase, mitochondrial 1B	-	HPRD,BioGRID	7525559 \|11602586
CYCS	CYC \| HCS	cytochrome c, somatic	-	HPRD,BioGRID	12243190
DCD	AIDD \| DCD-1 \| DSEP \| HCAP \| MGC71930 \| PIF	dermcidin	Affinity Capture-MS	BioGRID	17353931
DYNLT1	CW-1 \| MGC111571 \| TCTEL1 \| tctex-1	dynein, light chain, Tctex-type 1	-	HPRD	12009301
DYNLT1	CW-1 \| MGC111571 \| TCTEL1 \| tctex-1	dynein, light chain, Tctex-type 1	Tctex-1 interacts with hVDAC1.	BIND	12009301
DYNLT3	RP3 \| TCTE1L \| TCTEX1L	dynein, light chain, Tctex-type 3	-	HPRD,BioGRID	12009301
GABARAPL2	ATG8 \| GATE-16 \| GATE16 \| GEF-2 \| GEF2	GABA(A) receptor-associated protein-like 2	Affinity Capture-MS	BioGRID	17353931
GSN	DKFZp313L0718	gelsolin (amyloidosis, Finnish type)	-	HPRD,BioGRID	11039896
HK1	HK1-ta \| HK1-tb \| HK1-tc \| HKI \| HXK1	hexokinase 1	-	HPRD	10978502
HSPA9	CSA \| GRP75 \| HSPA9B \| MGC4500 \| MOT \| MOT2 \| MTHSP75 \| PBP74 \| mot-2	heat shock 70kDa protein 9 (mortalin)	PBP74 interacts with hVDAC1.	BIND	12009301
KIF5B	KINH \| KNS \| KNS1 \| UKHC	kinesin family member 5B	Affinity Capture-MS	BioGRID	17353931
MCC	DKFZp762O1615 \| FLJ38893 \| FLJ46755 \| MCC1	mutated in colorectal cancers	Affinity Capture-MS	BioGRID	17353931
MCL1	BCL2L3 \| EAT \| MCL1L \| MCL1S \| MGC104264 \| MGC1839 \| TM	myeloid cell leukemia sequence 1 (BCL2-related)	Reconstituted Complex	BioGRID	15637055
PANK2	C20orf48 \| FLJ17232 \| HARP \| HSS \| MGC15053 \| NBIA1 \| PKAN	pantothenate kinase 2	Affinity Capture-MS	BioGRID	17353931
PRKCE	MGC125656 \| MGC125657 \| PKCE \| nPKC-epsilon	protein kinase C, epsilon	-	HPRD,BioGRID	12663490
RAF1	CRAF \| NS5 \| Raf-1 \| c-Raf	v-raf-1 murine leukemia viral oncogene homolog 1	Affinity Capture-Western	BioGRID	12079506
TOMM20	KIAA0016 \| MAS20 \| MGC117367 \| MOM19 \| TOM20	translocase of outer mitochondrial membrane 20 homolog (yeast)	-	HPRD,BioGRID	9119086
TRAF6	MGC:3310 \| RNF85	TNF receptor-associated factor 6	Affinity Capture-MS	BioGRID	17353931

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CALCIUM SIGNALING PATHWAY	178	134	All SZGR 2.0 genes in this pathway
KEGG PARKINSONS DISEASE	133	78	All SZGR 2.0 genes in this pathway
KEGG HUNTINGTONS DISEASE	185	109	All SZGR 2.0 genes in this pathway
REACTOME MITOCHONDRIAL PROTEIN IMPORT	58	24	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF PROTEINS	518	242	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN	663	425	All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA UP	305	185	All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN	362	238	All SZGR 2.0 genes in this pathway
BIDUS METASTASIS UP	214	134	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 DN	378	231	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP	552	347	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND SERUM DEPRIVATION UP	211	136	All SZGR 2.0 genes in this pathway
GALLUZZI PERMEABILIZE MITOCHONDRIA	43	31	All SZGR 2.0 genes in this pathway
GALLUZZI PREVENT MITOCHONDIAL PERMEABILIZATION	22	16	All SZGR 2.0 genes in this pathway
SCHLOSSER MYC TARGETS AND SERUM RESPONSE UP	47	32	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP	358	245	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN	584	395	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
ALCALA APOPTOSIS	88	60	All SZGR 2.0 genes in this pathway
GOTZMANN EPITHELIAL TO MESENCHYMAL TRANSITION DN	206	136	All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION DN	187	122	All SZGR 2.0 genes in this pathway
YAGI AML RELAPSE PROGNOSIS	35	24	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN	309	206	All SZGR 2.0 genes in this pathway
FLECHNER PBL KIDNEY TRANSPLANT OK VS DONOR UP	151	100	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN	546	351	All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION DN	337	230	All SZGR 2.0 genes in this pathway
HASLINGER B CLL WITH 17P13 DELETION	21	15	All SZGR 2.0 genes in this pathway
FERRANDO T ALL WITH MLL ENL FUSION UP	87	67	All SZGR 2.0 genes in this pathway
WANG TARGETS OF MLL CBP FUSION DN	45	31	All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR	293	193	All SZGR 2.0 genes in this pathway
YAGI AML SURVIVAL	129	87	All SZGR 2.0 genes in this pathway
FAELT B CLL WITH VH3 21 UP	44	30	All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS POSTNATAL	63	50	All SZGR 2.0 genes in this pathway
LU AGING BRAIN DN	153	120	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN	504	323	All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS DN	215	132	All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE DN	261	183	All SZGR 2.0 genes in this pathway
ZAMORA NOS2 TARGETS DN	96	71	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS DN	141	92	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN	911	527	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN	1011	592	All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN	270	181	All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS UP	425	253	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR UP	294	199	All SZGR 2.0 genes in this pathway
ALONSO METASTASIS UP	198	128	All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE DN	264	159	All SZGR 2.0 genes in this pathway
CHANG CORE SERUM RESPONSE UP	212	128	All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN MYELOMA VS MATURE B LYMPHOCYTE	101	76	All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN ACTIVATED B LYMPHOCYTE	81	66	All SZGR 2.0 genes in this pathway
ZHAN VARIABLE EARLY DIFFERENTIATION GENES DN	30	19	All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE UP	442	263	All SZGR 2.0 genes in this pathway
FONTAINE FOLLICULAR THYROID ADENOMA DN	68	45	All SZGR 2.0 genes in this pathway
GUTIERREZ MULTIPLE MYELOMA UP	35	24	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC UP	72	53	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN DN	150	99	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR DN	254	158	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP D	280	158	All SZGR 2.0 genes in this pathway
BILANGES RAPAMYCIN SENSITIVE VIA TSC1 AND TSC2	73	37	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-183	520	526	m8	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-26	832	838	1A	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	832	838	1A	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-324-5p	88	95	1A,m8	hsa-miR-324-5p	CGCAUCCCCUAGGGCAUUGGUGU
miR-485-3p	616	622	1A	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-493-5p	9	15	1A	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-7	769	776	1A,m8	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: VDAC1