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Gene: PPM1N |
Gene summary for PPM1N |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PPM1N | Gene ID | 147699 |
| Gene name | protein phosphatase, Mg2+/Mn2+ dependent 1N (putative) | |
| Gene Alias | PPM1N | |
| Cytomap | 19q13.32 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q8N819 |
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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 |
| 147699 | PPM1N | C21 | Human | Oral cavity | OSCC | 8.63e-03 | 1.12e-01 | 0.2678 |
| 147699 | PPM1N | C30 | Human | Oral cavity | OSCC | 1.33e-05 | 2.05e-01 | 0.3055 |
| 147699 | PPM1N | C43 | Human | Oral cavity | OSCC | 3.67e-07 | 2.30e-01 | 0.1704 |
| 147699 | PPM1N | C46 | Human | Oral cavity | OSCC | 3.03e-37 | 6.68e-01 | 0.1673 |
| 147699 | PPM1N | C51 | Human | Oral cavity | OSCC | 3.00e-03 | 2.05e-01 | 0.2674 |
| 147699 | PPM1N | C08 | Human | Oral cavity | OSCC | 2.10e-06 | 1.18e-01 | 0.1919 |
| 147699 | PPM1N | C09 | Human | Oral cavity | OSCC | 7.87e-03 | 1.23e-01 | 0.1431 |
| 147699 | PPM1N | LN22 | Human | Oral cavity | OSCC | 5.72e-05 | 4.85e-01 | 0.1733 |
| 147699 | PPM1N | LN46 | Human | Oral cavity | OSCC | 1.33e-22 | 6.82e-01 | 0.1666 |
| 147699 | PPM1N | LP15 | Human | Oral cavity | LP | 4.58e-04 | 7.61e-01 | 0.2174 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:004312218 | Oral cavity | OSCC | regulation of I-kappaB kinase/NF-kappaB signaling | 155/7305 | 249/18723 | 7.79e-14 | 4.14e-12 | 155 |
| GO:000724910 | Oral cavity | OSCC | I-kappaB kinase/NF-kappaB signaling | 169/7305 | 281/18723 | 4.69e-13 | 2.25e-11 | 169 |
| GO:000647015 | Oral cavity | OSCC | protein dephosphorylation | 162/7305 | 281/18723 | 1.56e-10 | 4.56e-09 | 162 |
| GO:00163119 | Oral cavity | OSCC | dephosphorylation | 220/7305 | 417/18723 | 6.33e-09 | 1.34e-07 | 220 |
| GO:001605510 | Oral cavity | OSCC | Wnt signaling pathway | 227/7305 | 444/18723 | 1.10e-07 | 1.87e-06 | 227 |
| GO:019873810 | Oral cavity | OSCC | cell-cell signaling by wnt | 227/7305 | 446/18723 | 1.75e-07 | 2.86e-06 | 227 |
| GO:003011110 | Oral cavity | OSCC | regulation of Wnt signaling pathway | 165/7305 | 328/18723 | 1.87e-05 | 1.80e-04 | 165 |
| GO:00902639 | Oral cavity | OSCC | positive regulation of canonical Wnt signaling pathway | 62/7305 | 106/18723 | 3.72e-05 | 3.31e-04 | 62 |
| GO:006082810 | Oral cavity | OSCC | regulation of canonical Wnt signaling pathway | 128/7305 | 253/18723 | 1.11e-04 | 8.16e-04 | 128 |
| GO:006007010 | Oral cavity | OSCC | canonical Wnt signaling pathway | 148/7305 | 303/18723 | 2.89e-04 | 1.82e-03 | 148 |
| GO:00301779 | Oral cavity | OSCC | positive regulation of Wnt signaling pathway | 73/7305 | 140/18723 | 1.06e-03 | 5.46e-03 | 73 |
| GO:004312219 | Oral cavity | LP | regulation of I-kappaB kinase/NF-kappaB signaling | 103/4623 | 249/18723 | 4.48e-09 | 1.90e-07 | 103 |
| GO:000724917 | Oral cavity | LP | I-kappaB kinase/NF-kappaB signaling | 110/4623 | 281/18723 | 4.94e-08 | 1.70e-06 | 110 |
| GO:001605515 | Oral cavity | LP | Wnt signaling pathway | 140/4623 | 444/18723 | 5.80e-04 | 5.35e-03 | 140 |
| GO:019873815 | Oral cavity | LP | cell-cell signaling by wnt | 140/4623 | 446/18723 | 7.12e-04 | 6.38e-03 | 140 |
| GO:006082815 | Oral cavity | LP | regulation of canonical Wnt signaling pathway | 82/4623 | 253/18723 | 3.23e-03 | 2.18e-02 | 82 |
| GO:003011115 | Oral cavity | LP | regulation of Wnt signaling pathway | 103/4623 | 328/18723 | 3.29e-03 | 2.21e-02 | 103 |
| GO:000647016 | Oral cavity | LP | protein dephosphorylation | 89/4623 | 281/18723 | 4.60e-03 | 2.93e-02 | 89 |
| GO:009026315 | Oral cavity | LP | positive regulation of canonical Wnt signaling pathway | 38/4623 | 106/18723 | 6.67e-03 | 3.89e-02 | 38 |
| GO:006007015 | Oral cavity | LP | canonical Wnt signaling pathway | 94/4623 | 303/18723 | 6.97e-03 | 3.96e-02 | 94 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| PPM1N | SNV | Missense_Mutation | novel | c.754N>C | p.Ser252Pro | p.S252P | Q8N819 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-S3-AA11-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | letrozole | CR |
| PPM1N | SNV | Missense_Mutation | rs367762624 | c.625G>C | p.Glu209Gln | p.E209Q | Q8N819 | protein_coding | deleterious(0.03) | possibly_damaging(0.5) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PPM1N | SNV | Missense_Mutation | c.944G>A | p.Ser315Asn | p.S315N | Q8N819 | protein_coding | deleterious(0.01) | probably_damaging(0.946) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| PPM1N | SNV | Missense_Mutation | novel | c.941G>A | p.Gly314Asp | p.G314D | Q8N819 | protein_coding | deleterious(0.01) | possibly_damaging(0.566) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PPM1N | SNV | Missense_Mutation | novel | c.1226N>G | p.Lys409Arg | p.K409R | Q8N819 | protein_coding | tolerated(0.09) | benign(0.048) | TCGA-CK-4948-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PPM1N | SNV | Missense_Mutation | c.1145N>T | p.Gly382Val | p.G382V | Q8N819 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CK-4950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | folfox | SD | |
| PPM1N | SNV | Missense_Mutation | c.1203N>T | p.Gln401His | p.Q401H | Q8N819 | protein_coding | deleterious(0.04) | possibly_damaging(0.76) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PPM1N | SNV | Missense_Mutation | c.859N>A | p.Gly287Arg | p.G287R | Q8N819 | protein_coding | tolerated(0.31) | benign(0.18) | TCGA-G4-6586-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PPM1N | SNV | Missense_Mutation | novel | c.1156N>C | p.Asp386His | p.D386H | Q8N819 | protein_coding | tolerated(0.55) | benign(0.003) | TCGA-AG-3883-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PPM1N | SNV | Missense_Mutation | novel | c.965T>C | p.Ile322Thr | p.I322T | Q8N819 | protein_coding | deleterious(0.01) | possibly_damaging(0.821) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
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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 |
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