SZGR2

Summary ?

GeneID	5537
Symbol	PPP6C
Synonyms	PP6\|PP6C
Description	protein phosphatase 6 catalytic subunit
Reference	MIM:612725\|HGNC:HGNC:9323\|Ensembl:ENSG00000119414\|HPRD:02141\|Vega:OTTHUMG00000020671
Gene type	protein-coding
Map location	9q33.3
Pascal p-value	0.318
Sherlock p-value	0.587
Fetal beta	-0.143
DMG	1 (# studies)
eGene	Caudate basal ganglia Putamen basal ganglia

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
Expression	Meta-analysis of gene expression	P value: 1.866

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg03801144	9	127951957	PPP6C		-0.018	0.83	DMG:Nishioka_2013

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs620677	9	127819261	PPP6C	ENSG00000119414.7	4.09463E-6	0.01	132957	gtex_brain_putamen_basal
rs687654	9	127833905	PPP6C	ENSG00000119414.7	1.90289E-6	0.01	118313	gtex_brain_putamen_basal
rs650599	9	127849318	PPP6C	ENSG00000119414.7	3.38774E-7	0.01	102900	gtex_brain_putamen_basal
rs58809143	9	127961613	PPP6C	ENSG00000119414.7	1.26497E-6	0.01	-9395	gtex_brain_putamen_basal
rs405631	9	127968496	PPP6C	ENSG00000119414.7	2.1975E-6	0.01	-16278	gtex_brain_putamen_basal
rs500438	9	127970845	PPP6C	ENSG00000119414.7	1.71951E-6	0.01	-18627	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
FAM164A	0.94	0.96
RSG17	0.94	0.95
TTC13	0.93	0.95
HMGCR	0.93	0.94
RNF2	0.92	0.95
PRKAR2B	0.92	0.95
ARPC5	0.91	0.95
RUFY3	0.91	0.93
SH3GLB1	0.91	0.90
NCUBE1	0.91	0.94

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
HLA-F	-0.72	-0.81
AIFM3	-0.71	-0.80
TSC22D4	-0.69	-0.81
MT-CO2	-0.69	-0.88
AF347015.27	-0.69	-0.85
HEPN1	-0.69	-0.78
AF347015.31	-0.68	-0.86
AF347015.33	-0.68	-0.86
ALDOC	-0.67	-0.72
S100B	-0.67	-0.81

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		16716191
GO:0004722	protein serine/threonine phosphatase activity	IDA		16716191
GO:0016787	hydrolase activity	IEA		-
GO:0030145	manganese ion binding	IEA		-
GO:0046872	metal ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000082	G1/S transition of mitotic cell cycle	TAS		9013334
GO:0006470	protein amino acid dephosphorylation	IDA		16716191
GO:0007049	cell cycle	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005829	cytosol	IDA		16716191
GO:0005737	cytoplasm	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
TURASHVILI BREAST LOBULAR CARCINOMA VS LOBULAR NORMAL UP	94	59	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	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
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN	537	339	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 UP	121	71	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2A DN	141	84	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER WITH LOH IN CHR9Q	116	71	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS	775	494	All SZGR 2.0 genes in this pathway
SAKAI TUMOR INFILTRATING MONOCYTES DN	81	51	All SZGR 2.0 genes in this pathway
LU IL4 SIGNALING	94	56	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP	198	132	All SZGR 2.0 genes in this pathway
KYNG WERNER SYNDROM AND NORMAL AGING DN	225	124	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	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
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
CARD MIR302A TARGETS	77	62	All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS	239	156	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-103/107	261	267	1A	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
				hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
				hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
				hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-15/16/195/424/497	95	101	m8	hsa-miR-15a^brain	UAGCAGCACAUAAUGGUUUGUG
				hsa-miR-16^brain	UAGCAGCACGUAAAUAUUGGCG
				hsa-miR-15b^brain	UAGCAGCACAUCAUGGUUUACA
				hsa-miR-195^SZ	UAGCAGCACAGAAAUAUUGGC
				hsa-miR-424	CAGCAGCAAUUCAUGUUUUGAA
				hsa-miR-497	CAGCAGCACACUGUGGUUUGU
miR-17-5p/20/93.mr/106/519.d	89	95	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-208	245	251	1A	hsa-miR-208	AUAAGACGAGCAAAAAGCUUGU
miR-214	97	103	1A	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-221/222	267	273	m8	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	267	273	m8	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-31	113	119	m8	hsa-miR-31	AGGCAAGAUGCUGGCAUAGCUG
miR-335	272	278	m8	hsa-miR-335^brain	UCAAGAGCAAUAACGAAAAAUGU
miR-495	156	162	m8	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-499	245	251	1A	hsa-miR-499	UUAAGACUUGCAGUGAUGUUUAA
miR-93.hd/291-3p/294/295/302/372/373/520	88	94	m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

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: PPP6C