SZGR2

Summary ?

GeneID	6118
Symbol	RPA2
Synonyms	REPA2\|RP-A p32\|RP-A p34\|RPA32
Description	replication protein A2
Reference	MIM:179836\|HGNC:HGNC:10290\|Ensembl:ENSG00000117748\|HPRD:01566\|Vega:OTTHUMG00000003915
Gene type	protein-coding
Map location	1p35
Pascal p-value	0.137
Sherlock p-value	0.303
Fetal beta	0.453
DMG	2 (# studies)
eGene	Anterior cingulate cortex BA24 Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Hippocampus Hypothalamus Nucleus accumbens basal ganglia Putamen basal ganglia Myers' cis & trans Meta

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.	2
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

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg26339992	1	28241106	RPA2	1.78E-6	-0.402	0.008	DMG:Wockner_2014
cg09844983	1	28240714	RPA2	6.04E-10	-0.016	9.07E-7	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs8079075	chr17	38010814	RPA2	6118		0.18		trans
rs17185038	1	28219658	RPA2	ENSG00000117748.5	1.51449E-8	0.01	21599	gtex_brain_ba24
rs17185052	1	28241083	RPA2	ENSG00000117748.5	2.53049E-7	0.01	174	gtex_brain_ba24
rs28904914	1	28217354	RPA2	ENSG00000117748.5	1.04024E-6	0	23903	gtex_brain_putamen_basal
rs17185038	1	28219658	RPA2	ENSG00000117748.5	3.27453E-10	0	21599	gtex_brain_putamen_basal
rs17257252	1	28220484	RPA2	ENSG00000117748.5	1.04024E-6	0	20773	gtex_brain_putamen_basal
rs17185052	1	28241083	RPA2	ENSG00000117748.5	2.23183E-9	0	174	gtex_brain_putamen_basal

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
POLR2I	0.88	0.81
SSNA1	0.85	0.78
POLR2L	0.85	0.78
TCEB2	0.84	0.74
DGCR6L	0.84	0.80
FAM128B	0.83	0.71
RABAC1	0.82	0.76
C16orf13	0.82	0.76
GAMT	0.82	0.74
TIMM13	0.82	0.74

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
FLT1	-0.36	-0.35
SDPR	-0.36	-0.33
NFAT5	-0.33	-0.27
LRP1B	-0.33	-0.27
MYSM1	-0.33	-0.26
COBLL1	-0.33	-0.26
MAN2A1	-0.33	-0.30
PLCL1	-0.32	-0.28
FMNL2	-0.32	-0.28
VPS13C	-0.32	-0.25

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ACP5	MGC117378 \| TRAP	acid phosphatase 5, tartrate resistant	Two-hybrid	BioGRID	16169070
C1orf103	FLJ11269 \| RIF1 \| RP11-96K19.1	chromosome 1 open reading frame 103	Two-hybrid	BioGRID	16169070
C7orf64	DKFZP564O0523 \| DKFZp686D1651 \| HSPC304	chromosome 7 open reading frame 64	Two-hybrid	BioGRID	16169070
CCNO	CCNU \| FLJ22422 \| UDG2 \| UNG2	cyclin O	-	HPRD,BioGRID	10393198 \|11081631\|11081631
CDC2	CDC28A \| CDK1 \| DKFZp686L20222 \| MGC111195	cell division cycle 2, G1 to S and G2 to M	-	HPRD	1318195
COPS6	CSN6 \| MOV34-34KD	COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)	Two-hybrid	BioGRID	16169070
CREBBP	CBP \| KAT3A \| RSTS	CREB binding protein	Affinity Capture-Western	BioGRID	17525332
CRMP1	DPYSL1 \| DRP-1 \| DRP1	collapsin response mediator protein 1	Two-hybrid	BioGRID	16169070
EEF1A1	CCS-3 \| CCS3 \| EEF-1 \| EEF1A \| EF-Tu \| EF1A \| FLJ25721 \| GRAF-1EF \| HNGC:16303 \| LENG7 \| MGC102687 \| MGC131894 \| MGC16224 \| PTI1 \| eEF1A-1	eukaryotic translation elongation factor 1 alpha 1	Two-hybrid	BioGRID	16169070
GAPDH	G3PD \| GAPD \| MGC88685	glyceraldehyde-3-phosphate dehydrogenase	Two-hybrid	BioGRID	16169070
GOLM1	C9orf155 \| FLJ22634 \| FLJ23608 \| GOLPH2 \| GP73 \| PSEC0257 \| bA379P1.3	golgi membrane protein 1	Two-hybrid	BioGRID	16169070
HERPUD1	HERP \| KIAA0025 \| Mif1 \| SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	Two-hybrid	BioGRID	16169070
HUS1	-	HUS1 checkpoint homolog (S. pombe)	Hus1 interacts with RPA32.	BIND	15897895
KIAA1377	-	KIAA1377	Two-hybrid	BioGRID	16169070
KIN	BTCD \| KIN17	KIN, antigenic determinant of recA protein homolog (mouse)	Co-fractionation	BioGRID	12754299
MCM2	BM28 \| CCNL1 \| CDCL1 \| D3S3194 \| KIAA0030 \| MGC10606 \| MITOTIN \| cdc19	minichromosome maintenance complex component 2	-	HPRD,BioGRID	12614612
MCM3	HCC5 \| MGC1157 \| P1-MCM3 \| P1.h \| RLFB	minichromosome maintenance complex component 3	Two-hybrid	BioGRID	12614612
MCM4	CDC21 \| CDC54 \| MGC33310 \| P1-CDC21 \| hCdc21	minichromosome maintenance complex component 4	Two-hybrid	BioGRID	12614612
MCM5	CDC46 \| MGC5315 \| P1-CDC46	minichromosome maintenance complex component 5	Two-hybrid	BioGRID	12614612
MED31	3110004H13Rik \| CGI-125 \| FLJ27436 \| FLJ36714 \| Soh1	mediator complex subunit 31	Two-hybrid	BioGRID	16169070
MEN1	MEAI \| SCG2	multiple endocrine neoplasia I	-	HPRD,BioGRID	12509449
ORC1L	HSORC1 \| ORC1 \| PARC1	origin recognition complex, subunit 1-like (yeast)	Two-hybrid	BioGRID	12614612
ORC2L	ORC2	origin recognition complex, subunit 2-like (yeast)	-	HPRD,BioGRID	12614612
ORC4L	ORC4 \| ORC4P	origin recognition complex, subunit 4-like (yeast)	Two-hybrid	BioGRID	12614612
ORC5L	ORC5 \| ORC5P \| ORC5T	origin recognition complex, subunit 5-like (yeast)	Two-hybrid	BioGRID	12614612
PRKDC	DNA-PKcs \| DNAPK \| DNPK1 \| HYRC \| HYRC1 \| XRCC7 \| p350	protein kinase, DNA-activated, catalytic polypeptide	DNA-PKcs interacts with RPA2.	BIND	11000264
PRKDC	DNA-PKcs \| DNAPK \| DNPK1 \| HYRC \| HYRC1 \| XRCC7 \| p350	protein kinase, DNA-activated, catalytic polypeptide	-	HPRD,BioGRID	10064605 \|11731442
RAD1	HRAD1 \| REC1	RAD1 homolog (S. pombe)	An unspecified isoform of Rad1 interacts with RPA32.	BIND	15897895
RAD52	-	RAD52 homolog (S. cerevisiae)	Affinity Capture-Western	BioGRID	12139939
RAD9A	RAD9	RAD9 homolog A (S. pombe)	Rad9 interacts with RPA32.	BIND	15897895
RPA1	HSSB \| REPA1 \| RF-A \| RP-A \| RPA70	replication protein A1, 70kDa	-	HPRD	9461578 \|12754299
RPA1	HSSB \| REPA1 \| RF-A \| RP-A \| RPA70	replication protein A1, 70kDa	Affinity Capture-Western Co-crystal Structure	BioGRID	10064605 \|11927569
RPA3	REPA3	replication protein A3, 14kDa	Co-crystal Structure Co-purification	BioGRID	9461578 \|11927569
RPA3	REPA3	replication protein A3, 14kDa	-	HPRD	9461578 \|11173472\|11081631
RPA4	HSU24186 \| MGC120333 \| MGC120334	replication protein A4, 34kDa	Affinity Capture-Western Two-hybrid	BioGRID	7760808
RPLP1	FLJ27448 \| MGC5215 \| P1 \| RPP1	ribosomal protein, large, P1	Two-hybrid	BioGRID	16169070
SERTAD3	RBT1	SERTA domain containing 3	-	HPRD,BioGRID	10982866
STAT3	APRF \| FLJ20882 \| HIES \| MGC16063	signal transducer and activator of transcription 3 (acute-phase response factor)	-	HPRD,BioGRID	10875894
TLE1	ESG \| ESG1 \| GRG1	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	Two-hybrid	BioGRID	16169070
TP53BP1	53BP1 \| FLJ41424 \| MGC138366 \| p202	tumor protein p53 binding protein 1	Affinity Capture-MS Affinity Capture-Western	BioGRID	15856006
TUBB2A	TUBB \| TUBB2 \| dJ40E16.7	tubulin, beta 2A	Two-hybrid	BioGRID	16169070
UNC119	HRG4	unc-119 homolog (C. elegans)	Two-hybrid	BioGRID	16169070
UNG	DGU \| DKFZp781L1143 \| HIGM4 \| UDG \| UNG1 \| UNG15 \| UNG2	uracil-DNA glycosylase	-	HPRD,BioGRID	9045683
UTP14A	KIAA0266 \| NY-CO-16 \| SDCCAG16 \| dJ537K23.3	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	Two-hybrid	BioGRID	16169070
XPA	XP1 \| XPAC	xeroderma pigmentosum, complementation group A	-	HPRD,BioGRID	7565690 \|11081631\|11081631
XRCC6	CTC75 \| CTCBF \| G22P1 \| KU70 \| ML8 \| TLAA	X-ray repair complementing defective repair in Chinese hamster cells 6	Affinity Capture-Western	BioGRID	10064605

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG DNA REPLICATION	36	21	All SZGR 2.0 genes in this pathway
KEGG NUCLEOTIDE EXCISION REPAIR	44	25	All SZGR 2.0 genes in this pathway
KEGG MISMATCH REPAIR	23	14	All SZGR 2.0 genes in this pathway
KEGG HOMOLOGOUS RECOMBINATION	28	17	All SZGR 2.0 genes in this pathway
PID FANCONI PATHWAY	47	28	All SZGR 2.0 genes in this pathway
PID ATR PATHWAY	39	25	All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF THE PRE REPLICATIVE COMPLEX	31	16	All SZGR 2.0 genes in this pathway
REACTOME MEIOSIS	116	81	All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE	421	253	All SZGR 2.0 genes in this pathway
REACTOME PROCESSIVE SYNTHESIS ON THE LAGGING STRAND	15	10	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 HOMOLOGOUS RECOMBINATION REPAIR OF REPLICATION INDEPENDENT DOUBLE STRAND BREAKS	17	11	All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTION COUPLED NER TC NER	45	24	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 NUCLEOTIDE EXCISION REPAIR	51	27	All SZGR 2.0 genes in this pathway
REACTOME REPAIR SYNTHESIS FOR GAP FILLING BY DNA POL IN TC NER	14	11	All SZGR 2.0 genes in this pathway
REACTOME SYNTHESIS OF DNA	92	53	All SZGR 2.0 genes in this pathway
REACTOME DOUBLE STRAND BREAK REPAIR	24	14	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 MITOTIC M M G1 PHASES	172	98	All SZGR 2.0 genes in this pathway
REACTOME DNA REPAIR	112	59	All SZGR 2.0 genes in this pathway
REACTOME CHROMOSOME MAINTENANCE	122	80	All SZGR 2.0 genes in this pathway
REACTOME GLOBAL GENOMIC NER GG NER	35	20	All SZGR 2.0 genes in this pathway
REACTOME FORMATION OF INCISION COMPLEX IN GG NER	23	11	All SZGR 2.0 genes in this pathway
REACTOME MEIOTIC RECOMBINATION	86	62	All SZGR 2.0 genes in this pathway
REACTOME LAGGING STRAND SYNTHESIS	19	12	All SZGR 2.0 genes in this pathway
REACTOME DNA REPLICATION	192	110	All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF ATR IN RESPONSE TO REPLICATION STRESS	38	18	All SZGR 2.0 genes in this pathway
REACTOME TELOMERE MAINTENANCE	75	57	All SZGR 2.0 genes in this pathway
REACTOME REMOVAL OF THE FLAP INTERMEDIATE FROM THE C STRAND	10	8	All SZGR 2.0 genes in this pathway
REACTOME EXTENSION OF TELOMERES	27	17	All SZGR 2.0 genes in this pathway
REACTOME G2 M CHECKPOINTS	45	23	All SZGR 2.0 genes in this pathway
REACTOME S PHASE	109	66	All SZGR 2.0 genes in this pathway
REACTOME DNA STRAND ELONGATION	30	18	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
SLEBOS HEAD AND NECK CANCER WITH HPV UP	84	43	All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN	800	473	All SZGR 2.0 genes in this pathway
AMUNDSON GENOTOXIC SIGNATURE	105	68	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 BREAST CANCER LIT INT NETWORK	101	73	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 UP	209	139	All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES	648	385	All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES	230	137	All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPLICATION GENES	147	87	All SZGR 2.0 genes in this pathway
KENNY CTNNB1 TARGETS UP	50	30	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
FLECHNER PBL KIDNEY TRANSPLANT REJECTED VS OK UP	63	48	All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP	203	135	All SZGR 2.0 genes in this pathway
APRELIKOVA BRCA1 TARGETS	49	33	All SZGR 2.0 genes in this pathway
JACKSON DNMT1 TARGETS UP	77	57	All SZGR 2.0 genes in this pathway
KALMA E2F1 TARGETS	11	7	All SZGR 2.0 genes in this pathway
LOPES METHYLATED IN COLON CANCER DN	28	26	All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED	728	415	All SZGR 2.0 genes in this pathway
LABBE TARGETS OF TGFB1 AND WNT3A UP	111	70	All SZGR 2.0 genes in this pathway
RAY TUMORIGENESIS BY ERBB2 CDC25A DN	159	105	All SZGR 2.0 genes in this pathway
MUELLER PLURINET	299	189	All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS UP	374	247	All SZGR 2.0 genes in this pathway
HINATA NFKB TARGETS FIBROBLAST UP	84	60	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR DN	277	166	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
WONG EMBRYONIC STEM CELL CORE	335	193	All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE S	162	86	All SZGR 2.0 genes in this pathway
LU EZH2 TARGETS DN	414	237	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN	918	550	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN	882	538	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP	570	339	All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS UP	107	72	All SZGR 2.0 genes in this pathway
ZHOU CELL CYCLE GENES IN IR RESPONSE 6HR	85	49	All SZGR 2.0 genes in this pathway
ZHOU CELL CYCLE GENES IN IR RESPONSE 24HR	128	73	All SZGR 2.0 genes in this pathway

Gene Page: RPA2