SZGR2

Summary ?

GeneID	5034
Symbol	P4HB
Synonyms	CLCRP1\|DSI\|ERBA2L\|GIT\|P4Hbeta\|PDI\|PDIA1\|PHDB\|PO4DB\|PO4HB\|PROHB
Description	prolyl 4-hydroxylase subunit beta
Reference	MIM:176790\|HGNC:HGNC:8548\|Ensembl:ENSG00000185624\|HPRD:07181\|Vega:OTTHUMG00000150269
Gene type	protein-coding
Map location	17q25
Pascal p-value	0.867
Sherlock p-value	1
DMG	1 (# studies)
eGene	Cerebellum Cortex
Support	RNA AND PROTEIN SYNTHESIS

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.7758

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg15882999	17	79818726	P4HB		-0.02	0.76	DMG:Nishioka_2013

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
ICMT	0.84	0.81
SPOCK2	0.80	0.78
SLC7A8	0.79	0.84
INPP4B	0.79	0.77
PEG3AS	0.78	0.75
KIAA1324L	0.78	0.77
RNF6	0.78	0.80
SGPP2	0.78	0.74
SRPR	0.78	0.84
CYLD	0.78	0.79

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
EMID1	-0.39	-0.41
KLHL1	-0.37	-0.04
WDR86	-0.37	-0.36
SCUBE1	-0.36	-0.30
SLA	-0.36	-0.02
DACT1	-0.36	-0.03
TMEM108	-0.35	-0.09
MPPED1	-0.35	-0.13
NEUROD2	-0.35	-0.14
NEUROD6	-0.34	-0.17

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003756	protein disulfide isomerase activity	TAS		2846539
GO:0005515	protein binding	IPI		17055437 \|17353931
GO:0004656	procollagen-proline 4-dioxygenase activity	IDA		7753822
GO:0016853	isomerase activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0018401	peptidyl-proline hydroxylation to 4-hydroxy-L-proline	IDA		7753822
GO:0045454	cell redox homeostasis	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005792	microsome	IEA		-
GO:0005793	ER-Golgi intermediate compartment	IDA		15308636
GO:0005788	endoplasmic reticulum lumen	IEA		-
GO:0005576	extracellular region	NAS		14718574
GO:0005783	endoplasmic reticulum	IEA		-
GO:0005783	endoplasmic reticulum	TAS		3034602
GO:0009986	cell surface	IDA		12493773
GO:0005886	plasma membrane	IEA		-
GO:0042470	melanosome	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CD2BP2	FWP010 \| LIN1 \| Snu40 \| U5-52K	CD2 (cytoplasmic tail) binding protein 2	Affinity Capture-MS	BioGRID	17353931
COL1A1	OI4	collagen, type I, alpha 1	-	HPRD	1339453
COL1A2	OI4	collagen, type I, alpha 2	-	HPRD,BioGRID	10329688
CUL2	MGC131970	cullin 2	Affinity Capture-MS	BioGRID	17353931
EIF4A2	BM-010 \| DDX2B \| EIF4A \| EIF4F	eukaryotic translation initiation factor 4A, isoform 2	Affinity Capture-MS	BioGRID	17353931
ELF3	EPR-1 \| ERT \| ESE-1 \| ESX	E74-like factor 3 (ets domain transcription factor, epithelial-specific )	Affinity Capture-MS	BioGRID	17353931
ERO1L	ERO1-alpha	ERO1-like (S. cerevisiae)	-	HPRD,BioGRID	11707400
ERO1LB	-	ERO1-like beta (S. cerevisiae)	-	HPRD,BioGRID	11847130
FEZ1	-	fasciculation and elongation protein zeta 1 (zygin I)	Two-hybrid	BioGRID	16169070
P4HA2	-	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II	-	HPRD	7753822
P4HA3	-	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	-	HPRD	12874193 \|14500733
PTN	HARP \| HBGF8 \| HBNF \| NEGF1	pleiotrophin	Two-hybrid	BioGRID	16169070
PUF60	FIR \| FLJ31379 \| RoBPI \| SIAHBP1	poly-U binding splicing factor 60KDa	Affinity Capture-MS	BioGRID	17353931
TG	AITD3 \| TGN	thyroglobulin	-	HPRD,BioGRID	10636893
TNFRSF14	ATAR \| HVEA \| HVEM \| LIGHTR \| TR2	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	Affinity Capture-MS	BioGRID	17353931
TRIP6	MGC10556 \| MGC10558 \| MGC29959 \| MGC3837 \| MGC4423 \| OIP1 \| ZRP-1	thyroid hormone receptor interactor 6	Affinity Capture-MS	BioGRID	17353931
UBQLN1	DA41 \| DSK2 \| FLJ90054 \| PLIC-1 \| XDRP1	ubiquilin 1	-	HPRD,BioGRID	12095988

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
BIOCARTA HIF PATHWAY	15	12	All SZGR 2.0 genes in this pathway
BIOCARTA VITCB PATHWAY	11	6	All SZGR 2.0 genes in this pathway
ST INTEGRIN SIGNALING PATHWAY	82	62	All SZGR 2.0 genes in this pathway
REACTOME EXTRACELLULAR MATRIX ORGANIZATION	87	42	All SZGR 2.0 genes in this pathway
REACTOME COLLAGEN FORMATION	58	31	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS	478	302	All SZGR 2.0 genes in this pathway
REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT	46	37	All SZGR 2.0 genes in this pathway
REACTOME LIPOPROTEIN METABOLISM	28	24	All SZGR 2.0 genes in this pathway
REACTOME CHYLOMICRON MEDIATED LIPID TRANSPORT	16	15	All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN	634	384	All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER UP	404	246	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 UP	380	236	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 UP	418	263	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR DN	214	133	All SZGR 2.0 genes in this pathway
CHOW RASSF1 TARGETS DN	29	19	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP	530	342	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 DN	378	231	All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER UP	181	108	All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 5	147	89	All SZGR 2.0 genes in this pathway
LI LUNG CANCER	41	30	All SZGR 2.0 genes in this pathway
LI AMPLIFIED IN LUNG CANCER	178	108	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE AUGMENTED BY MYC	108	74	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER DN	203	134	All SZGR 2.0 genes in this pathway
LIEN BREAST CARCINOMA METAPLASTIC	35	25	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP	283	177	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS B LYMPHOCYTE UP	78	51	All SZGR 2.0 genes in this pathway
ROSS AML WITH PML RARA FUSION	77	62	All SZGR 2.0 genes in this pathway
CHEN LUNG CANCER SURVIVAL	28	22	All SZGR 2.0 genes in this pathway
SHIPP DLBCL VS FOLLICULAR LYMPHOMA UP	45	30	All SZGR 2.0 genes in this pathway
GALE APL WITH FLT3 MUTATED DN	17	10	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA DN	408	274	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS LATE PROGENITOR	544	307	All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS UP	175	116	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY NO BLOOD UP	222	139	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP	487	303	All SZGR 2.0 genes in this pathway
RAMASWAMY METASTASIS UP	66	43	All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL	311	205	All SZGR 2.0 genes in this pathway
ZHONG SECRETOME OF LUNG CANCER AND FIBROBLAST	132	93	All SZGR 2.0 genes in this pathway
CAMPS COLON CANCER COPY NUMBER UP	92	45	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER ERBB2 UP	147	83	All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA DN	100	63	All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB UP	245	159	All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 12	30	20	All SZGR 2.0 genes in this pathway
JISON SICKLE CELL DISEASE UP	181	106	All SZGR 2.0 genes in this pathway
NGO MALIGNANT GLIOMA 1P LOH	17	13	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP	605	377	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
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN	418	245	All SZGR 2.0 genes in this pathway
PECE MAMMARY STEM CELL DN	146	88	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-188	201	207	m8	hsa-miR-188	CAUCCCUUGCAUGGUGGAGGGU
miR-204/211	200	206	m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	200	206	m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU

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: P4HB