SZGR2

Summary ?

GeneID	8502
Symbol	PKP4
Synonyms	p0071
Description	plakophilin 4
Reference	MIM:604276\|HGNC:HGNC:9026\|Ensembl:ENSG00000144283\|HPRD:05043\|Vega:OTTHUMG00000153969
Gene type	protein-coding
Map location	2q24.1
Pascal p-value	0.007
Sherlock p-value	0.066
eGene	Myers' cis & trans
Support	CELL ADHESION AND TRANSSYNAPTIC SIGNALING G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS CompositeSet Darnell FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.02395

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs2141326	chr2	28779227	PKP4	8502	0.08	trans
rs871872	chr2	28782263	PKP4	8502	0.06	trans
rs1733504	chr3	71372796	PKP4	8502	0.01	trans
rs1290499	chr3	71393339	PKP4	8502	0.15	trans
rs1295400	chr7	51138813	PKP4	8502	0.01	trans
rs758167	chr12	1915558	PKP4	8502	0.07	trans
rs10144695	chr14	49442442	PKP4	8502	0.19	trans
rs6518060	chr21	22427853	PKP4	8502	0.17	trans
rs9983417	chr21	22431220	PKP4	8502	0.15	trans

Section II. Transcriptome annotation

General gene expression (GTEx)

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
ANAPC2	0.93	0.93
BRF1	0.92	0.94
AC011498.3	0.92	0.93
SF4	0.92	0.92
CCDC137	0.91	0.92
OGFR	0.91	0.91
PPAN	0.90	0.90
PELP1	0.90	0.91
ATAD3A	0.90	0.92
ZNF653	0.89	0.91

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.80	-0.82
MT-CO2	-0.79	-0.81
AF347015.33	-0.77	-0.78
MT-CYB	-0.76	-0.79
AF347015.27	-0.76	-0.80
AF347015.21	-0.76	-0.82
AF347015.8	-0.75	-0.80
AF347015.2	-0.73	-0.77
AF347015.15	-0.73	-0.78
HIGD1B	-0.72	-0.75

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005488	binding	IEA		-
GO:0005515	protein binding	IEA		-
GO:0005198	structural molecule activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007155	cell adhesion	NAS		8937994
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005911	cell-cell junction	TAS		8937994

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
DAVICIONI MOLECULAR ARMS VS ERMS UP	332	228	All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 UP	408	247	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL UP	233	161	All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL DN	275	168	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN	536	332	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS DN	459	276	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP	536	340	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
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN	483	336	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP	414	287	All SZGR 2.0 genes in this pathway
DAWSON METHYLATED IN LYMPHOMA TCL1	59	45	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	All SZGR 2.0 genes in this pathway
WEI MIR34A TARGETS	148	97	All SZGR 2.0 genes in this pathway
LIAO METASTASIS	539	324	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY UP	236	139	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215	893	528	All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP	424	268	All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION	405	264	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA UP	98	64	All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP	203	135	All SZGR 2.0 genes in this pathway
GENTILE UV RESPONSE CLUSTER D5	39	26	All SZGR 2.0 genes in this pathway
GAJATE RESPONSE TO TRABECTEDIN DN	19	11	All SZGR 2.0 genes in this pathway
GENTILE UV HIGH DOSE DN	312	203	All SZGR 2.0 genes in this pathway
KEEN RESPONSE TO ROSIGLITAZONE DN	106	68	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR	681	420	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP	953	554	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN	1011	592	All SZGR 2.0 genes in this pathway
GAVIN FOXP3 TARGETS CLUSTER P3	160	103	All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS UP	425	253	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL DN	216	143	All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A5	70	32	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA	43	27	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS UP	74	45	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP	518	299	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 9	76	45	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	All SZGR 2.0 genes in this pathway
VANOEVELEN MYOGENESIS SIN3A TARGETS	220	133	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-125/351	150	156	1A	hsa-miR-125b^brain	UCCCUGAGACCCUAACUUGUGA
miR-125/351	150	156	1A	hsa-miR-125a^brain	UCCCUGAGACCCUUUAACCUGUG
miR-150	170	177	1A,m8	hsa-miR-150	UCUCCCAACCCUUGUACCAGUG
miR-183	481	487	m8	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-192/215	298	305	1A,m8	hsa-miR-192	CUGACCUAUGAAUUGACAGCC
miR-192/215	298	305	1A,m8	hsa-miR-215	AUGACCUAUGAAUUGACAGAC
miR-218	629	636	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-23	329	336	1A,m8	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	329	336	1A,m8	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-323	328	335	1A,m8	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-34/449	694	701	1A,m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC

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: PKP4