Gene Page:PPP6C

Summary?
GeneID 5537
Symbol PPP6C
Synonyms PP6|PP6C
描述 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
硬膜basal ganglia

Gene in Data Sources
Gene set name Method of gene set 描述 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 Pvalue: 1.866

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) β(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)

Not available

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 去term Evidence Neuro keywords PubMed ID
GO:0005506 iron ion binding IEA -
GO:0005515 protein binding 新闻学会 16716191
GO:0004722 protein serine/threonine phosphatase activity IDA 16716191
GO:0016787 hydrolase activity IEA -
GO:0030145 manganese ion binding IEA -
GO:0046872 金属离子结合 IEA -
Biological process 去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 去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
UTR start UTR end Match method
miR-103/107 261 267 1A hsa-miR-103brain AGCAGCAUUGUACAGGGCUAUGA
hsa-miR-107brain AGCAGCAUUGUACAGGGCUAUCA
hsa-miR-103brain AGCAGCAUUGUACAGGGCUAUGA
hsa-miR-107brain AGCAGCAUUGUACAGGGCUAUCA
miR-15/16/195/424/497 95 101 m8 hsa-miR-15abrain UAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brain UAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrain UAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZ 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-20abrain UAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106a AAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZ UAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZ CAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519d CAAAGUGCCUCCCUUUAGAGUGU
miR-208 245 251 1A hsa-miR-208 AUAAGACGAGCAAAAAGCUUGU
miR-214 97 103 1A hsa-miR-214brain ACAGCAGGCACAGACAGGCAG
miR-221/222 267 273 m8 hsa-miR-221brain AGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brain AGCUACAUCUGGCUACUGGGUCUC
miR-31 113 119 m8 hsa-miR-31 AGGCAAGAUGCUGGCAUAGCUG
miR-335 272 278 m8 hsa-miR-335brain UCAAGAGCAAUAACGAAAAAUGU
miR-495 156 162 m8 hsa-miR-495brain 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-93brain 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