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Gene: PPM1D |
Gene summary for PPM1D |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PPM1D | Gene ID | 8493 |
| Gene name | protein phosphatase, Mg2+/Mn2+ dependent 1D | |
| Gene Alias | IDDGIP | |
| Cytomap | 17q23.2 | |
| Gene Type | protein-coding | GO ID | GO:0000086 | UniProtAcc | A0A0S2Z4M2 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 8493 | PPM1D | LZE4T | Human | Esophagus | ESCC | 2.44e-10 | 3.27e-01 | 0.0811 |
| 8493 | PPM1D | LZE7T | Human | Esophagus | ESCC | 6.68e-03 | 2.13e-01 | 0.0667 |
| 8493 | PPM1D | LZE20T | Human | Esophagus | ESCC | 1.86e-03 | 1.27e-01 | 0.0662 |
| 8493 | PPM1D | LZE24T | Human | Esophagus | ESCC | 1.56e-18 | 3.74e-01 | 0.0596 |
| 8493 | PPM1D | LZE21T | Human | Esophagus | ESCC | 3.29e-04 | 2.95e-01 | 0.0655 |
| 8493 | PPM1D | P1T-E | Human | Esophagus | ESCC | 2.40e-08 | 5.14e-01 | 0.0875 |
| 8493 | PPM1D | P2T-E | Human | Esophagus | ESCC | 4.58e-38 | 6.77e-01 | 0.1177 |
| 8493 | PPM1D | P4T-E | Human | Esophagus | ESCC | 1.08e-05 | 1.65e-01 | 0.1323 |
| 8493 | PPM1D | P5T-E | Human | Esophagus | ESCC | 5.83e-05 | 6.27e-02 | 0.1327 |
| 8493 | PPM1D | P8T-E | Human | Esophagus | ESCC | 1.44e-15 | 2.35e-01 | 0.0889 |
| 8493 | PPM1D | P9T-E | Human | Esophagus | ESCC | 1.94e-05 | 1.57e-01 | 0.1131 |
| 8493 | PPM1D | P10T-E | Human | Esophagus | ESCC | 3.86e-11 | 2.22e-01 | 0.116 |
| 8493 | PPM1D | P11T-E | Human | Esophagus | ESCC | 1.29e-11 | 4.08e-01 | 0.1426 |
| 8493 | PPM1D | P12T-E | Human | Esophagus | ESCC | 2.08e-25 | 5.24e-01 | 0.1122 |
| 8493 | PPM1D | P15T-E | Human | Esophagus | ESCC | 9.23e-26 | 4.91e-01 | 0.1149 |
| 8493 | PPM1D | P16T-E | Human | Esophagus | ESCC | 1.77e-19 | 4.00e-01 | 0.1153 |
| 8493 | PPM1D | P20T-E | Human | Esophagus | ESCC | 7.86e-15 | 3.04e-01 | 0.1124 |
| 8493 | PPM1D | P21T-E | Human | Esophagus | ESCC | 9.89e-06 | 1.10e-01 | 0.1617 |
| 8493 | PPM1D | P22T-E | Human | Esophagus | ESCC | 2.03e-11 | 2.98e-01 | 0.1236 |
| 8493 | PPM1D | P23T-E | Human | Esophagus | ESCC | 8.75e-44 | 9.17e-01 | 0.108 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:004477216 | Esophagus | ESCC | mitotic cell cycle phase transition | 281/8552 | 424/18723 | 4.63e-18 | 4.45e-16 | 281 |
| GO:0071496111 | Esophagus | ESCC | cellular response to external stimulus | 215/8552 | 320/18723 | 4.29e-15 | 2.43e-13 | 215 |
| GO:0072331111 | Esophagus | ESCC | signal transduction by p53 class mediator | 121/8552 | 163/18723 | 9.61e-14 | 4.69e-12 | 121 |
| GO:0031668111 | Esophagus | ESCC | cellular response to extracellular stimulus | 168/8552 | 246/18723 | 4.93e-13 | 2.23e-11 | 168 |
| GO:0031669110 | Esophagus | ESCC | cellular response to nutrient levels | 148/8552 | 215/18723 | 4.58e-12 | 1.76e-10 | 148 |
| GO:0031667111 | Esophagus | ESCC | response to nutrient levels | 289/8552 | 474/18723 | 9.25e-12 | 3.47e-10 | 289 |
| GO:000931419 | Esophagus | ESCC | response to radiation | 277/8552 | 456/18723 | 4.42e-11 | 1.43e-09 | 277 |
| GO:0009267110 | Esophagus | ESCC | cellular response to starvation | 110/8552 | 156/18723 | 2.63e-10 | 7.37e-09 | 110 |
| GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| GO:004259419 | Esophagus | ESCC | response to starvation | 133/8552 | 197/18723 | 4.31e-10 | 1.14e-08 | 133 |
| GO:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
| GO:004277014 | Esophagus | ESCC | signal transduction in response to DNA damage | 117/8552 | 172/18723 | 2.38e-09 | 5.32e-08 | 117 |
| GO:00448394 | Esophagus | ESCC | cell cycle G2/M phase transition | 103/8552 | 148/18723 | 3.09e-09 | 6.67e-08 | 103 |
| GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
| GO:00000864 | Esophagus | ESCC | G2/M transition of mitotic cell cycle | 96/8552 | 137/18723 | 6.00e-09 | 1.23e-07 | 96 |
| GO:00400295 | Esophagus | ESCC | regulation of gene expression, epigenetic | 74/8552 | 105/18723 | 2.24e-07 | 3.42e-06 | 74 |
| GO:00063673 | Esophagus | ESCC | transcription initiation from RNA polymerase II promoter | 56/8552 | 77/18723 | 1.30e-06 | 1.59e-05 | 56 |
| GO:0030330110 | Esophagus | ESCC | DNA damage response, signal transduction by p53 class mediator | 53/8552 | 72/18723 | 1.34e-06 | 1.63e-05 | 53 |
| GO:000635211 | Esophagus | ESCC | DNA-templated transcription, initiation | 86/8552 | 130/18723 | 1.88e-06 | 2.19e-05 | 86 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0411524 | Esophagus | ESCC | p53 signaling pathway | 65/4205 | 74/8465 | 3.88e-12 | 6.50e-11 | 3.33e-11 | 65 |
| hsa0411534 | Esophagus | ESCC | p53 signaling pathway | 65/4205 | 74/8465 | 3.88e-12 | 6.50e-11 | 3.33e-11 | 65 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| PPM1D | SNV | Missense_Mutation | c.356N>G | p.His119Arg | p.H119R | O15297 | protein_coding | deleterious(0.03) | benign(0.104) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PPM1D | SNV | Missense_Mutation | rs772026101 | c.879A>C | p.Glu293Asp | p.E293D | O15297 | protein_coding | tolerated(0.15) | possibly_damaging(0.851) | TCGA-D8-A1X7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | ChemotherapyHormone Therapy | doxorubicine+cyclophosphamide+tamoxifen | SD |
| PPM1D | SNV | Missense_Mutation | c.1547C>T | p.Ser516Leu | p.S516L | O15297 | protein_coding | deleterious_low_confidence(0.01) | benign(0.033) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PPM1D | insertion | Frame_Shift_Ins | novel | c.1542_1543insGTAAA | p.Met515ValfsTer9 | p.M515Vfs*9 | O15297 | protein_coding | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| PPM1D | deletion | Frame_Shift_Del | rs766595966 | c.1529delN | p.Asn512IlefsTer2 | p.N512Ifs*2 | O15297 | protein_coding | TCGA-E2-A14O-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | arimidex | SD | ||
| PPM1D | SNV | Missense_Mutation | rs150055145 | c.1058N>A | p.Arg353Gln | p.R353Q | O15297 | protein_coding | tolerated(0.09) | possibly_damaging(0.711) | TCGA-VS-A8QA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PPM1D | SNV | Missense_Mutation | rs371199697 | c.1373N>A | p.Arg458Gln | p.R458Q | O15297 | protein_coding | tolerated_low_confidence(0.16) | benign(0.416) | TCGA-A6-6141-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fu | SD |
| PPM1D | SNV | Missense_Mutation | c.1255N>A | p.Val419Ile | p.V419I | O15297 | protein_coding | tolerated(0.51) | benign(0) | TCGA-AA-A01P-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| PPM1D | SNV | Missense_Mutation | c.1442C>T | p.Ala481Val | p.A481V | O15297 | protein_coding | deleterious_low_confidence(0.02) | benign(0.045) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD | |
| PPM1D | SNV | Missense_Mutation | novel | c.743N>A | p.Arg248Gln | p.R248Q | O15297 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 8493 | PPM1D | KINASE, SERINE THREONINE KINASE, ENZYME | DOXORUBICIN | DOXORUBICIN | 25466181 |
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