SZGR2

Summary ?

GeneID	5708
Symbol	PSMD2
Synonyms	P97\|RPN1\|S2\|TRAP2
Description	proteasome 26S subunit, non-ATPase 2
Reference	MIM:606223\|HGNC:HGNC:9559\|Ensembl:ENSG00000175166\|HPRD:05870\|Vega:OTTHUMG00000156796
Gene type	protein-coding
Map location	3q27.1
Pascal p-value	0.105
Sherlock p-value	0.003
TADA p-value	0.014
Fetal beta	-0.404
eGene	Cerebellar Hemisphere Nucleus accumbens basal ganglia Myers' cis & trans
Support	G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet Ascano FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:PGCnp	Genome-wide Association Study	GWAS
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0069

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
PSMD2	chr3	184025295	A	G	NM_002808	p.729M>V	missense			Schizophrenia	DNM:Fromer_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs17432613	chr1	18346091	PSMD2	5708		0.19		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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
FGD1	0.91	0.92
SARM1	0.89	0.91
GLT25D1	0.89	0.91
DTX4	0.89	0.92
ASXL1	0.89	0.90
UBAP2	0.89	0.89
CCDC120	0.89	0.90
FRMD4A	0.88	0.87
GPR173	0.88	0.90
ZMYM3	0.88	0.88

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.74	-0.87
AF347015.27	-0.73	-0.86
S100B	-0.73	-0.83
MT-CO2	-0.73	-0.87
AIFM3	-0.72	-0.75
AF347015.33	-0.72	-0.85
TSC22D4	-0.71	-0.77
HEPN1	-0.71	-0.75
MT-CYB	-0.71	-0.85
C5orf53	-0.70	-0.74

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005488	binding	IEA		-
GO:0005515	protein binding	IPI		11278995
GO:0030234	enzyme regulator activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0042176	regulation of protein catabolic process	IEA		-
GO:0031145	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process	EXP		11285280
GO:0051436	negative regulation of ubiquitin-protein ligase activity during mitotic cell cycle	EXP		15029244
GO:0051437	positive regulation of ubiquitin-protein ligase activity during mitotic cell cycle	EXP		12791267
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000502	proteasome complex	TAS		8811196
GO:0005829	cytosol	IEA		-
GO:0005838	proteasome regulatory particle	TAS		8774743

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
C1orf103	FLJ11269 \| RIF1 \| RP11-96K19.1	chromosome 1 open reading frame 103	Two-hybrid	BioGRID	16169070
MCC	DKFZp762O1615 \| FLJ38893 \| FLJ46755 \| MCC1	mutated in colorectal cancers	Affinity Capture-MS	BioGRID	17353931
NEK6	SID6-1512	NIMA (never in mitosis gene a)-related kinase 6	Affinity Capture-MS	BioGRID	17353931
PAAF1	FLJ11848 \| PAAF \| Rpn14 \| WDR71	proteasomal ATPase-associated factor 1	Affinity Capture-MS	BioGRID	17353931
PSMC1	MGC24583 \| MGC8541 \| P26S4 \| S4 \| p56	proteasome (prosome, macropain) 26S subunit, ATPase, 1	-	HPRD,BioGRID	10625621
PSMC2	MGC3004 \| MSS1 \| Nbla10058 \| S7	proteasome (prosome, macropain) 26S subunit, ATPase, 2	-	HPRD,BioGRID	10625621
PSMC4	MGC13687 \| MGC23214 \| MGC8570 \| MIP224 \| S6 \| TBP7	proteasome (prosome, macropain) 26S subunit, ATPase, 4	Affinity Capture-MS	BioGRID	17353931
PSMD10	dJ889N15.2 \| p28	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	Affinity Capture-MS	BioGRID	17353931
PSMD13	HSPC027 \| Rpn9 \| S11 \| p40.5	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	Affinity Capture-MS	BioGRID	17353931
PSMD5	KIAA0072 \| MGC23145 \| S5B	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	-	HPRD,BioGRID	10625621
PSMD6	KIAA0107 \| Rpn7 \| S10 \| SGA-113M \| p44S10	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	Affinity Capture-MS	BioGRID	17353931
PTN	HARP \| HBGF8 \| HBNF \| NEGF1	pleiotrophin	Two-hybrid	BioGRID	16169070
TNFRSF1A	CD120a \| FPF \| MGC19588 \| TBP1 \| TNF-R \| TNF-R-I \| TNF-R55 \| TNFAR \| TNFR1 \| TNFR55 \| TNFR60 \| p55 \| p55-R \| p60	tumor necrosis factor receptor superfamily, member 1A	-	HPRD,BioGRID	7601280 \|9126987
UBE3C	KIAA0010 \| KIAA10	ubiquitin protein ligase E3C	-	HPRD,BioGRID	12692129
UBLCP1	CPUB1 \| FLJ25267 \| MGC10067	ubiquitin-like domain containing CTD phosphatase 1	Two-hybrid	BioGRID	16189514
UNC119	HRG4	unc-119 homolog (C. elegans)	Two-hybrid	BioGRID	16169070
WDR8	FLJ20430 \| MGC99569	WD repeat domain 8	Affinity Capture-MS	BioGRID	17353931
ZBTB16	PLZF \| ZNF145	zinc finger and BTB domain containing 16	Two-hybrid	BioGRID	16169070

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG PROTEASOME	48	28	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY WNT	65	41	All SZGR 2.0 genes in this pathway
REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES	48	29	All SZGR 2.0 genes in this pathway
REACTOME ANTIGEN PROCESSING CROSS PRESENTATION	76	48	All SZGR 2.0 genes in this pathway
REACTOME ER PHAGOSOME PATHWAY	61	40	All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE	421	253	All SZGR 2.0 genes in this pathway
REACTOME ORC1 REMOVAL FROM CHROMATIN	67	37	All SZGR 2.0 genes in this pathway
REACTOME DOWNSTREAM SIGNALING EVENTS OF B CELL RECEPTOR BCR	97	66	All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF NF KAPPAB IN B CELLS	64	43	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY THE B CELL RECEPTOR BCR	126	90	All SZGR 2.0 genes in this pathway
REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT	51	31	All SZGR 2.0 genes in this pathway
REACTOME CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6	48	27	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF AMINO ACIDS AND DERIVATIVES	200	136	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF ORNITHINE DECARBOXYLASE ODC	49	33	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF APOPTOSIS	58	34	All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE MITOTIC	325	185	All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE CHECKPOINTS	124	70	All SZGR 2.0 genes in this pathway
REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION	65	40	All SZGR 2.0 genes in this pathway
REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE	57	35	All SZGR 2.0 genes in this pathway
REACTOME M G1 TRANSITION	81	45	All SZGR 2.0 genes in this pathway
REACTOME G1 S TRANSITION	112	63	All SZGR 2.0 genes in this pathway
REACTOME CDT1 ASSOCIATION WITH THE CDC6 ORC ORIGIN COMPLEX	56	31	All SZGR 2.0 genes in this pathway
REACTOME SYNTHESIS OF DNA	92	53	All SZGR 2.0 genes in this pathway
REACTOME AUTODEGRADATION OF THE E3 UBIQUITIN LIGASE COP1	51	30	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF MRNA	284	128	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA	330	155	All SZGR 2.0 genes in this pathway
REACTOME MITOTIC G1 G1 S PHASES	137	79	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF MITOTIC CELL CYCLE	85	46	All SZGR 2.0 genes in this pathway
REACTOME MITOTIC M M G1 PHASES	172	98	All SZGR 2.0 genes in this pathway
REACTOME ASSEMBLY OF THE PRE REPLICATIVE COMPLEX	65	36	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS	84	50	All SZGR 2.0 genes in this pathway
REACTOME DESTABILIZATION OF MRNA BY AUF1 HNRNP D0	53	31	All SZGR 2.0 genes in this pathway
REACTOME DNA REPLICATION	192	110	All SZGR 2.0 genes in this pathway
REACTOME APOPTOSIS	148	94	All SZGR 2.0 genes in this pathway
REACTOME HIV INFECTION	207	122	All SZGR 2.0 genes in this pathway
REACTOME HOST INTERACTIONS OF HIV FACTORS	132	81	All SZGR 2.0 genes in this pathway
REACTOME APC C CDH1 MEDIATED DEGRADATION OF CDC20 AND OTHER APC C CDH1 TARGETED PROTEINS IN LATE MITOSIS EARLY G1	72	38	All SZGR 2.0 genes in this pathway
REACTOME APC C CDC20 MEDIATED DEGRADATION OF MITOTIC PROTEINS	73	40	All SZGR 2.0 genes in this pathway
REACTOME AUTODEGRADATION OF CDH1 BY CDH1 APC C	64	34	All SZGR 2.0 genes in this pathway
REACTOME SCF BETA TRCP MEDIATED DEGRADATION OF EMI1	51	32	All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM	933	616	All SZGR 2.0 genes in this pathway
REACTOME ADAPTIVE IMMUNE SYSTEM	539	350	All SZGR 2.0 genes in this pathway
REACTOME CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION	251	156	All SZGR 2.0 genes in this pathway
REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION	212	129	All SZGR 2.0 genes in this pathway
REACTOME S PHASE	109	66	All SZGR 2.0 genes in this pathway
REACTOME SCFSKP2 MEDIATED DEGRADATION OF P27 P21	56	34	All SZGR 2.0 genes in this pathway
REACTOME VIF MEDIATED DEGRADATION OF APOBEC3G	52	30	All SZGR 2.0 genes in this pathway
WINTER HYPOXIA UP	92	57	All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP	285	181	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA UP	305	185	All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP	290	177	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP	557	331	All SZGR 2.0 genes in this pathway
NADERI BREAST CANCER PROGNOSIS UP	50	26	All SZGR 2.0 genes in this pathway
TOMIDA METASTASIS UP	26	13	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK HIGH VS LOW DN	32	21	All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX	795	478	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
HE PTEN TARGETS DN	7	6	All SZGR 2.0 genes in this pathway
BASSO B LYMPHOCYTE NETWORK	143	96	All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION DN	187	122	All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER METASTASIS DN	121	65	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
RHODES UNDIFFERENTIATED CANCER	69	44	All SZGR 2.0 genes in this pathway
ZHU CMV ALL UP	120	89	All SZGR 2.0 genes in this pathway
ZHU CMV 24 HR UP	93	65	All SZGR 2.0 genes in this pathway
PELLICCIOTTA HDAC IN ANTIGEN PRESENTATION UP	64	40	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP	973	570	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP	863	514	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN DN	249	165	All SZGR 2.0 genes in this pathway
ITO PTTG1 TARGETS DN	9	7	All SZGR 2.0 genes in this pathway
CHUNG BLISTER CYTOTOXICITY UP	134	84	All SZGR 2.0 genes in this pathway
CHANG CORE SERUM RESPONSE UP	212	128	All SZGR 2.0 genes in this pathway
HSIAO HOUSEKEEPING GENES	389	245	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S1	237	159	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP	756	494	All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP	682	440	All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 6 DN	38	19	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-495	112	118	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU

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: PSMD2