SZGR2

Summary ?

GeneID	23362
Symbol	PSD3
Synonyms	EFA6D\|EFA6R\|HCA67
Description	pleckstrin and Sec7 domain containing 3
Reference	MIM:614440\|HGNC:HGNC:19093\|Ensembl:ENSG00000156011\|HPRD:11462\|Vega:OTTHUMG00000163711
Gene type	protein-coding
Map location	8p21.3
Pascal p-value	9.249E-5
Sherlock p-value	0.5
Fetal beta	1.154
DMG	1 (# studies)
eGene	Cerebellum Myers' cis & trans
Support	INTRACELLULAR SIGNAL TRANSDUCTION G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	2
GSMA_I	Genome scan meta-analysis	Psr: 0.031
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.03086
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.00057
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg05835241	8	18448662	PSD3	2.68E-4	0.368	0.038	DMG:Wockner_2014
cg08040428	8	18870913	PSD3	3.762E-4	-0.362	0.043	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs10994209	chr10	61877705	PSD3	23362		0.16		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
DDX23	0.96	0.95
UBE2R2	0.95	0.95
POLR3D	0.95	0.95
ZNF259	0.95	0.96
PJA1	0.95	0.96
SPATS2	0.95	0.94
PA2G4	0.94	0.93
GPN1	0.94	0.93
SF3B2	0.94	0.94
NOC2L	0.94	0.94

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MT-CO2	-0.82	-0.90
AF347015.31	-0.82	-0.90
AF347015.33	-0.81	-0.90
FXYD1	-0.81	-0.91
AF347015.27	-0.80	-0.89
MT-CYB	-0.79	-0.88
AF347015.8	-0.78	-0.89
S100B	-0.77	-0.85
HIGD1B	-0.77	-0.88
IFI27	-0.77	-0.86

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005086	ARF guanyl-nucleotide exchange factor activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0032012	regulation of ARF protein signal transduction	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0045211	postsynaptic membrane	IEA	Synap, Neurotransmitter (GO term level: 5)	-
GO:0045202	synapse	IEA	neuron, Synap, Neurotransmitter, Glial (GO term level: 2)	-
GO:0005622	intracellular	IEA		-
GO:0005624	membrane fraction	IEA		-
GO:0005886	plasma membrane	IEA		-
GO:0030054	cell junction	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ENDOCYTOSIS	183	132	All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA DN	526	357	All SZGR 2.0 genes in this pathway
DAVICIONI MOLECULAR ARMS VS ERMS DN	182	111	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE DN	244	147	All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL UP	276	187	All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS DN	384	230	All SZGR 2.0 genes in this pathway
SCIBETTA KDM5B TARGETS DN	81	55	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP	162	116	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP	443	294	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 DN	229	142	All SZGR 2.0 genes in this pathway
VANHARANTA UTERINE FIBROID WITH 7Q DELETION UP	67	37	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS DN	193	112	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN	1024	594	All SZGR 2.0 genes in this pathway
SUNG METASTASIS STROMA UP	110	70	All SZGR 2.0 genes in this pathway
ROSS ACUTE MYELOID LEUKEMIA CBF	82	57	All SZGR 2.0 genes in this pathway
ROSS AML WITH AML1 ETO FUSION	76	55	All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR	293	193	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK DN	318	220	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 5	482	296	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN	191	123	All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN	940	425	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BRAIN DN	85	58	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE UP	97	61	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL A UP	84	52	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER POOR SURVIVAL UP	31	22	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING	246	152	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING	510	309	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP	338	225	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP	418	282	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 DN	245	150	All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER DN	238	145	All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 13	30	20	All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G123 DN	51	30	All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION	368	247	All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA2 UP	87	50	All SZGR 2.0 genes in this pathway
CHANDRAN METASTASIS DN	306	191	All SZGR 2.0 genes in this pathway
MIKKELSEN ES HCP WITH H3 UNMETHYLATED	63	31	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN	505	328	All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 DN	88	61	All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 DN	82	51	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP C	92	60	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 COMPLETE	227	151	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM A	182	108	All SZGR 2.0 genes in this pathway
ZWANG CLASS 3 TRANSIENTLY INDUCED BY EGF	222	159	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY	1839	928	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
let-7/98	821	827	1A	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-134	453	460	1A,m8	hsa-miR-134^brain	UGUGACUGGUUGACCAGAGGG
miR-135	6013	6019	m8	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
miR-135	6013	6019	m8	hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-136	6952	6959	1A,m8	hsa-miR-136	ACUCCAUUUGUUUUGAUGAUGGA
miR-138	5562	5568	1A	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-139	1362	1368	1A	hsa-miR-139^brain	UCUACAGUGCACGUGUCU
miR-143	856	862	m8	hsa-miR-143^brain	UGAGAUGAAGCACUGUAGCUCA
miR-145	382	388	m8	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-18	215	221	m8	hsa-miR-18a	UAAGGUGCAUCUAGUGCAGAUA
miR-18	215	221	m8	hsa-miR-18b	UAAGGUGCAUCUAGUGCAGUUA
miR-186	5157	5163	1A	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-23	438	444	1A	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	438	444	1A	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-26	4462	4469	1A,m8	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	4462	4469	1A,m8	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-30-5p	8090	8096	1A	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-335	167	174	1A,m8	hsa-miR-335^brain	UCAAGAGCAAUAACGAAAAAUGU
miR-338	578	584	1A	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-381	8129	8135	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-448	6084	6090	m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-495	139	145	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-496	8390	8397	1A,m8	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-9	5474	5480	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

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: PSD3