SZGR2

Summary ?

GeneID	8974
Symbol	P4HA2
Synonyms	-
Description	prolyl 4-hydroxylase subunit alpha 2
Reference	MIM:600608\|HGNC:HGNC:8547\|Ensembl:ENSG00000072682\|HPRD:11862\|Vega:OTTHUMG00000059647
Gene type	protein-coding
Map location	5q31
Pascal p-value	0.399
Sherlock p-value	1.018E-4
Fetal beta	-0.572
DMG	1 (# studies)
eGene	Putamen basal ganglia Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
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).	1
GSMA_I	Genome scan meta-analysis	Psr: 0.0032

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg09140281	5	131563492	P4HA2	4.973E-4	-0.366	0.047	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs6689013	chr1	186980817	P4HA2	8974		0.09		trans
rs7607798	chr2	102043108	P4HA2	8974		0.1		trans
rs1879328	chr3	46568156	P4HA2	8974		0.18		trans
rs7706288	chr5	141864248	P4HA2	8974		0.12		trans
rs3899870	chr13	97205717	P4HA2	8974		0.04		trans
rs9300361	chr13	97210272	P4HA2	8974		0.05		trans
rs16965683	chr15	38115683	P4HA2	8974		1.326E-4		trans
rs17283561	chrX	33355912	P4HA2	8974		0.17		trans
rs5975293	chrX	130948027	P4HA2	8974		0.18		trans
rs201959459	5	130864001	P4HA2	ENSG00000072682.14	2.703E-6	0.04	767007	gtex_brain_putamen_basal
rs25884	5	131412238	P4HA2	ENSG00000072682.14	3.434E-6	0.04	218770	gtex_brain_putamen_basal
rs45236	5	131440620	P4HA2	ENSG00000072682.14	3.03E-6	0.04	190388	gtex_brain_putamen_basal
rs269900	5	131482244	P4HA2	ENSG00000072682.14	3.03E-6	0.04	148764	gtex_brain_putamen_basal
rs2550973	5	131511141	P4HA2	ENSG00000072682.14	3.001E-6	0.04	119867	gtex_brain_putamen_basal
rs201381512	5	131511399	P4HA2	ENSG00000072682.14	2.009E-6	0.04	119609	gtex_brain_putamen_basal
rs152056	5	131517482	P4HA2	ENSG00000072682.14	2.662E-6	0.04	113526	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
AGGF1	0.93	0.93
RAB6A	0.92	0.92
ARMCX3	0.92	0.92
YWHAB	0.91	0.89
BTRC	0.91	0.90
C5orf22	0.90	0.90
SERINC1	0.90	0.90
CLTC	0.90	0.90
VPS41	0.90	0.90
UCHL5	0.90	0.89

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
FXYD1	-0.63	-0.58
EIF4EBP3	-0.63	-0.66
MT-CO2	-0.62	-0.58
AF347015.21	-0.62	-0.53
HIGD1B	-0.62	-0.59
AF347015.31	-0.61	-0.59
ENHO	-0.61	-0.67
AF347015.2	-0.61	-0.56
TLCD1	-0.60	-0.57
PLA2G5	-0.59	-0.56

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005506	iron ion binding	IEA		-
GO:0005515	protein binding	IPI		14667819
GO:0004656	procollagen-proline 4-dioxygenase activity	TAS		9211872
GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	IEA		-
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	IEA		-
GO:0009055	electron carrier activity	TAS		9211872
GO:0016491	oxidoreductase activity	IEA		-
GO:0031418	L-ascorbic acid binding	IEA		-
GO:0046872	metal ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0019538	protein metabolic process	IEA		-
GO:0055114	oxidation reduction	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005788	endoplasmic reticulum lumen	IEA		-
GO:0005783	endoplasmic reticulum	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ARGININE AND PROLINE METABOLISM	54	39	All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP	783	507	All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP	579	346	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
UDAYAKUMAR MED1 TARGETS DN	240	171	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP	162	116	All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA UP	171	112	All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA BY DMOG UP	130	85	All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A TARGETS DN	91	58	All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A AND HIF2A TARGETS DN	104	72	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP	633	376	All SZGR 2.0 genes in this pathway
PROVENZANI METASTASIS DN	136	94	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP	443	294	All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS UP	77	62	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION DN	234	147	All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN UP	239	157	All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION UP	126	78	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER UP	227	137	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS UP	769	437	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP	811	508	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY DN	382	224	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR UP	176	115	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
SWEET KRAS TARGETS UP	84	51	All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP	207	145	All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR	293	193	All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT UP	89	61	All SZGR 2.0 genes in this pathway
MENSE HYPOXIA UP	98	71	All SZGR 2.0 genes in this pathway
TRAYNOR RETT SYNDROM DN	19	14	All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS UP	175	116	All SZGR 2.0 genes in this pathway
LEONARD HYPOXIA	47	35	All SZGR 2.0 genes in this pathway
SEMENZA HIF1 TARGETS	36	32	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 4	307	185	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
WEST ADRENOCORTICAL TUMOR UP	294	199	All SZGR 2.0 genes in this pathway
PODAR RESPONSE TO ADAPHOSTIN UP	147	98	All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA DN	100	63	All SZGR 2.0 genes in this pathway
WINTER HYPOXIA METAGENE	242	168	All SZGR 2.0 genes in this pathway
MOOTHA PGC	420	269	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D DN	252	155	All SZGR 2.0 genes in this pathway
TOOKER GEMCITABINE RESISTANCE DN	122	84	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN	457	302	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3	349	234	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3	210	148	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 8	49	36	All SZGR 2.0 genes in this pathway
SASSON RESPONSE TO GONADOTROPHINS UP	91	59	All SZGR 2.0 genes in this pathway
SASSON RESPONSE TO FORSKOLIN UP	90	58	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA MESENCHYMAL	216	130	All SZGR 2.0 genes in this pathway
QI HYPOXIA	140	96	All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS DN	242	146	All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS UP	217	131	All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS GROUP1	136	76	All SZGR 2.0 genes in this pathway
WIEDERSCHAIN TARGETS OF BMI1 AND PCGF2	57	39	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN	882	538	All SZGR 2.0 genes in this pathway
FARDIN HYPOXIA 11	32	29	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 7	403	240	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38	337	236	All SZGR 2.0 genes in this pathway
NABA ECM REGULATORS	238	125	All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED	753	411	All SZGR 2.0 genes in this pathway
NABA MATRISOME	1028	559	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	266	272	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-124/506	257	263	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	257	263	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-129-5p	367	373	1A	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	367	373	1A	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-30-5p	320	327	1A,m8	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-9	302	308	m8	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: P4HA2