Gene: PPM1D

LinkedOmicsKB © 2022-2023 Zhang Lab

Basic information

Full name
protein phosphatase, Mg2+/Mn2+ dependent 1D
Ensembl
ENSG00000170836.12
Summary
The protein encoded by this gene is a member of the PP2C family of Ser/Thr protein phosphatases. PP2C family members are known to be negative regulators of cell stress response pathways. The expression of this gene is induced in a p53-dependent manner in response to various environmental stresses. While being induced by tumor suppressor protein TP53/p53, this phosphatase negatively regulates the activity of p38 MAP kinase, MAPK/p38, through which it reduces the phosphorylation of p53, and in turn suppresses p53-mediated transcription and apoptosis. This phosphatase thus mediates a feedback regulation of p38-p53 signaling that contributes to growth inhibition and the suppression of stress induced apoptosis. This gene is located in a chromosomal region known to be amplified in breast cancer. The amplification of this gene has been detected in both breast cancer cell line and primary breast tumors, which suggests a role of this gene in cancer development. [provided by RefSeq, Jul 2008]
Annotation
Cancer driver (Oncogene) Phosphatase

Protein product

Phosphosites on the primary protein product

Tumor and normal comparison

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Signed p-values
Data type
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
RNA-1.1e-24-4.2e-21---1.3e-7-8.9e-24-7.3e-33--1.1e-4-
protein-0.72-----0.72-0.39---

* P-values are from Wilcoxon rank sum test and can be clicked to show the box plots. Positive values mean higher abundance in tumor. BRCA and GBM do not have normal samples.

mRNA expression at gene level
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC7.588.599.51010.51111.512log2(RSEM+1)tumornormal
Protein expression
BRCAGBMHNSCCLSCCLUADPDACUCEC1314151617181920212223log2(MS1 intensity)tumornormal

* Mild outlier: filled circle; Extreme outlier: empty circle.

Phenotype and mutation association

Manhattan plot summarizing associations of phenotypes and mutations across all cohorts and omics data types

BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC0123456789101112130-1-2-3-4-5-6-7-8-9-10-11-12-13Pan-cancer01234567891011120-1-2-3-4-5-6-7-8-9-10-11-12proteinRNASCNVclinicalpathwaycell typegenomicmutation-log10 of P-value

* Data points of significant associations above and below the dotted lines can be hovered to show the phenotype.

Associations of the protein abundance of PPM1D with phenotypes and mutations

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Signed p-values
Phenotype
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
HALLMARK_G2M_CHECKPOINT1.9e-33.5e-3---0.410.0150.65--0.76
cibersort: B cell naive2.7e-30.11---0.840.0820.17--0.076
HALLMARK_MITOTIC_SPINDLE4.7e-34.6e-4---0.420.690.51--0.35
HALLMARK_E2F_TARGETS5.2e-36.5e-3---0.770.0140.44--1
xcell: Plasmacytoid dendritic cell6.8e-34.1e-4---0.45-0.630.57--0.092
SBS7b (UVR)0.0110.14---0.16----0.13
HALLMARK_MYC_TARGETS_V10.0230.022----0.950.0130.88--0.83
HALLMARK_PI3K_AKT_MTOR_SIGNALING0.0249.6e-4---0.044-0.35-0.62--0.25
Clinical: Tumor_necrosis0.024-----0.10.12---
SBS5 (unknown)0.0341.4e-3----0.510.640.41--0.35
Showing 1 to 10 of 256 rows

* P-values could be from test for Spearman correlation, Wilcoxon rank sum test, Jonckheere-Terpstra trend test or Cox regression depending on the data type. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Cis-association

Associations between omics data of PPM1D

BRCA0.350.010.53proteinmRNASCNVmethylationCCRCC-0.17-0.060.04proteinmRNASCNVmethylationCOAD0.39proteinmRNASCNVmethylationGBM-0.200.40-0.24proteinmRNASCNVmethylationHNSCC-0.04-0.45-0.22-0.200.46-0.02proteinmRNASCNVmethylationLSCC0.49-0.130.31-0.320.47-0.28proteinmRNASCNVmethylationLUAD0.630.050.35-0.110.32-0.01proteinmRNASCNVmethylationOV0.52proteinmRNASCNVmethylationPDAC-0.040.52-0.13proteinmRNASCNVmethylationUCEC0.55-0.530.40-0.300.23-0.06proteinmRNASCNVmethylation

* The numbers are Spearman correlation coefficients and can be clicked to show the scatter plots. The color and size of the circles correlate with the coefficients.

Trans-association

Associations of the protein abundance of PPM1D and the protein abundance of other genes

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Signed p-values
Gene
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
No matching records found

* P-values are from test for Spearman correlation. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Gene set enrichment analysis

Submit genes and the common logarithm of the p-values of their association with to WebGestalt.