Summary ?
GeneID5531
SymbolPPP4C
SynonymsPP-X|PP4|PP4C|PPH3|PPP4|PPX
Descriptionprotein phosphatase 4 catalytic subunit
ReferenceMIM:602035|HGNC:HGNC:9319|Ensembl:ENSG00000149923|HPRD:03615|Vega:OTTHUMG00000132113
Gene typeprotein-coding
Map location16p11.2
Pascal p-value3.932E-6
Sherlock p-value0.82
Fetal beta1.228
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CNV:YESCopy number variation studiesManual curation
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.01775 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0033 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg119703011630087888PPP4C3.2E-10-0.0377.03E-7DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs4114866chr66257660PPP4C55310.1trans
rs3851513chr66274160PPP4C55310.05trans
rs2906115chr121248067PPP4C55310.01trans

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
GenePearson's Correlation Spearman's Correlation
PSD30.900.93
APPL10.900.93
AC010896.10.890.91
RABGAP1L0.890.92
LPGAT10.890.92
DMXL20.890.91
LMBRD20.880.91
AKAP110.880.92
RAB11FIP20.880.91
HIPK30.880.91
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C19orf36-0.57-0.64
FXYD1-0.56-0.65
RAB34-0.54-0.66
GSDMD-0.54-0.64
CST3-0.54-0.64
GATSL3-0.54-0.60
HIGD1B-0.54-0.65
TLCD1-0.53-0.61
DCXR-0.53-0.62
EIF4EBP3-0.53-0.61

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004704NF-kappaB-inducing kinase activityNAS9837938 
GO:0005506iron ion bindingIEA-
GO:0005515protein bindingIPI17353931 
GO:0004722protein serine/threonine phosphatase activityNAS9837938 
GO:0016787hydrolase activityIEA-
GO:0030145manganese ion bindingIEA-
GO:0046872metal ion bindingNAS-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000226microtubule cytoskeleton organizationNAS-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005813centrosomeNAS-
GO:0005634nucleusNAS-
GO:0005737cytoplasmIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
BAT3BAG-6 | BAG6 | D6S52E | G3HLA-B associated transcript 3Affinity Capture-MSBioGRID17353931 
CCDC6D10S170 | FLJ32286 | H4 | PTC | TPC | TST1coiled-coil domain containing 6Affinity Capture-MSBioGRID17353931 |18715871 
CCT299D8.1 | CCT-beta | CCTB | MGC142074 | MGC142076 | PRO1633 | TCP-1-betachaperonin containing TCP1, subunit 2 (beta)Affinity Capture-MSBioGRID16085932 |18715871 
CCT3CCT-gamma | CCTG | PIG48 | TCP-1-gamma | TRIC5chaperonin containing TCP1, subunit 3 (gamma)Affinity Capture-MSBioGRID16085932 |18715871 
CCT4CCT-DELTA | Cctd | MGC126164 | MGC126165 | SRBchaperonin containing TCP1, subunit 4 (delta)Affinity Capture-MSBioGRID16085932 |18715871 
CCT5CCT-epsilon | CCTE | KIAA0098 | TCP-1-epsilonchaperonin containing TCP1, subunit 5 (epsilon)Affinity Capture-MSBioGRID16085932 |18715871 
CCT6ACCT-zeta | CCT-zeta-1 | CCT6 | Cctz | HTR3 | MGC126214 | MGC126215 | MoDP-2 | TCP-1-zeta | TCP20 | TCPZ | TTCP20chaperonin containing TCP1, subunit 6A (zeta 1)Affinity Capture-MSBioGRID16085932 |18715871 
CCT7CCT-ETA | Ccth | MGC110985 | Nip7-1 | TCP-1-etachaperonin containing TCP1, subunit 7 (eta)Affinity Capture-MSBioGRID16085932 |18715871 
CCT8C21orf112 | Cctq | D21S246 | KIAA0002 | PRED71chaperonin containing TCP1, subunit 8 (theta)Affinity Capture-MSBioGRID16085932 
DHX38DDX38 | KIAA0224 | PRP16 | PRPF16DEAH (Asp-Glu-Ala-His) box polypeptide 38Affinity Capture-MSBioGRID18715871 
GEMIN4DKFZp434B131 | DKFZp434D174 | HC56 | HCAP1 | HHRF-1 | p97gem (nuclear organelle) associated protein 4Affinity Capture-WesternBioGRID12668731 
HDAC3HD3 | RPD3 | RPD3-2histone deacetylase 3PPP4C (PP4C) interacts with HDAC3.BIND15805470 
IGBP1ALPHA-4 | IBP1immunoglobulin (CD79A) binding protein 1-HPRD,BioGRID9647778 
JUNAP-1 | AP1 | c-Junjun oncogeneReconstituted ComplexBioGRID9837938 
NFKB1DKFZp686C01211 | EBP-1 | KBF1 | MGC54151 | NF-kappa-B | NFKB-p105 | NFKB-p50 | p105nuclear factor of kappa light polypeptide gene enhancer in B-cells 1-HPRD,BioGRID9837938 
PPP2CBPP2CBprotein phosphatase 2 (formerly 2A), catalytic subunit, beta isoformAffinity Capture-MSBioGRID17353931 
PPP2R1AMGC786 | PR65Aprotein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoformAffinity Capture-MSBioGRID17353931 |18715871 
PPP2R5DB56D | MGC2134 | MGC8949protein phosphatase 2, regulatory subunit B', delta isoformAffinity Capture-MSBioGRID18715871 
PPP4R1PP4(Rmeg) | PP4R1protein phosphatase 4, regulatory subunit 1-HPRD,BioGRID10026142 
PPP4R2MGC131930protein phosphatase 4, regulatory subunit 2-HPRD,BioGRID10769191 
PPP4R2MGC131930protein phosphatase 4, regulatory subunit 2-HPRD10769191 |12668731 
PPP4R4KIAA1622 | PP4R4protein phosphatase 4, regulatory subunit 4Affinity Capture-MS
Affinity Capture-Western
Reconstituted Complex
BioGRID18715871 
RELC-Relv-rel reticuloendotheliosis viral oncogene homolog (avian)-HPRD,BioGRID9837938 
RELAMGC131774 | NFKB3 | p65v-rel reticuloendotheliosis viral oncogene homolog A (avian)-HPRD,BioGRID9837938 
SMEK1FLFL1 | KIAA2010 | MSTP033 | PP4R3A | smk-1 | smk1SMEK homolog 1, suppressor of mek1 (Dictyostelium)Affinity Capture-MS
Reconstituted Complex
BioGRID16085932 |17353931 
|18715871 
SMEK2FLFL2 | FLJ31474 | KIAA1387 | PP4R3B | PSY2 | smk1SMEK homolog 2, suppressor of mek1 (Dictyostelium)Affinity Capture-MSBioGRID16085932 |17353931 
|18715871 
SMN1BCD541 | SMA | SMA1 | SMA2 | SMA3 | SMA4 | SMA@ | SMN | SMNT | T-BCD541survival of motor neuron 1, telomericAffinity Capture-WesternBioGRID12668731 
TCP1CCT-alpha | CCT1 | CCTa | D6S230E | TCP-1-alphat-complex 1Affinity Capture-MSBioGRID16085932 |18715871 
TIPRLMGC3794 | TIP | TIP41 | dJ69E11.3TIP41, TOR signaling pathway regulator-like (S. cerevisiae)Affinity Capture-MS
Reconstituted Complex
BioGRID16085932 |17353931 
TMSB4XFX | PTMB4 | TB4X | TMSB4thymosin beta 4, X-linked-HPRD,BioGRID9647778 
TP53FLJ92943 | LFS1 | TRP53 | p53tumor protein p53Reconstituted ComplexBioGRID9837938 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
BORCZUK MALIGNANT MESOTHELIOMA UP 305185All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530342All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443294All SZGR 2.0 genes in this pathway
CREIGHTON AKT1 SIGNALING VIA MTOR DN 2316All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE UP 13493All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP 380213All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN 514330All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN 309206All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION 475313All SZGR 2.0 genes in this pathway
CROMER METASTASIS DN 8158All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP 198132All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229713All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 2D DN 6435All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871505All SZGR 2.0 genes in this pathway
KESHELAVA MULTIPLE DRUG RESISTANCE 8856All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S1 237159All SZGR 2.0 genes in this pathway
WONG EMBRYONIC STEM CELL CORE 335193All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-12845521A,m8hsa-miR-128aUCACAGUGAACCGGUCUCUUUU
hsa-miR-128bUCACAGUGAACCGGUCUCUUUC
miR-274652m8hsa-miR-27abrainUUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrainUUCACAGUGGCUAAGUUCUGC