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Gene: PPM1L |
Gene summary for PPM1L |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PPM1L | Gene ID | 151742 |
| Gene name | protein phosphatase, Mg2+/Mn2+ dependent 1L | |
| Gene Alias | PP2C-epsilon | |
| Cytomap | 3q25.33-q26.1 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q5SGD2 |
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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 |
| 151742 | PPM1L | CCI_1 | Human | Cervix | CC | 8.96e-05 | 6.43e-01 | 0.528 |
| 151742 | PPM1L | CCI_2 | Human | Cervix | CC | 1.63e-06 | 1.10e+00 | 0.5249 |
| 151742 | PPM1L | LZE22D1 | Human | Esophagus | HGIN | 1.03e-04 | 1.17e-01 | 0.0595 |
| 151742 | PPM1L | LZE24T | Human | Esophagus | ESCC | 5.60e-15 | 3.82e-01 | 0.0596 |
| 151742 | PPM1L | P1T-E | Human | Esophagus | ESCC | 3.57e-06 | 4.24e-01 | 0.0875 |
| 151742 | PPM1L | P2T-E | Human | Esophagus | ESCC | 3.15e-10 | 1.70e-01 | 0.1177 |
| 151742 | PPM1L | P4T-E | Human | Esophagus | ESCC | 3.33e-10 | 2.67e-01 | 0.1323 |
| 151742 | PPM1L | P8T-E | Human | Esophagus | ESCC | 1.19e-08 | 3.96e-01 | 0.0889 |
| 151742 | PPM1L | P10T-E | Human | Esophagus | ESCC | 4.32e-17 | 3.30e-01 | 0.116 |
| 151742 | PPM1L | P12T-E | Human | Esophagus | ESCC | 1.56e-13 | 8.81e-02 | 0.1122 |
| 151742 | PPM1L | P16T-E | Human | Esophagus | ESCC | 5.58e-12 | 1.13e-01 | 0.1153 |
| 151742 | PPM1L | P20T-E | Human | Esophagus | ESCC | 5.24e-03 | 3.82e-02 | 0.1124 |
| 151742 | PPM1L | P22T-E | Human | Esophagus | ESCC | 1.73e-02 | 3.02e-02 | 0.1236 |
| 151742 | PPM1L | P23T-E | Human | Esophagus | ESCC | 7.44e-06 | 3.36e-01 | 0.108 |
| 151742 | PPM1L | P26T-E | Human | Esophagus | ESCC | 2.44e-04 | 3.85e-02 | 0.1276 |
| 151742 | PPM1L | P27T-E | Human | Esophagus | ESCC | 1.17e-19 | 2.84e-01 | 0.1055 |
| 151742 | PPM1L | P28T-E | Human | Esophagus | ESCC | 2.26e-05 | 2.23e-02 | 0.1149 |
| 151742 | PPM1L | P30T-E | Human | Esophagus | ESCC | 1.81e-16 | 7.77e-01 | 0.137 |
| 151742 | PPM1L | P31T-E | Human | Esophagus | ESCC | 1.17e-03 | 7.79e-03 | 0.1251 |
| 151742 | PPM1L | P36T-E | Human | Esophagus | ESCC | 3.92e-02 | 1.62e-02 | 0.1187 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:00064708 | Cervix | CC | protein dephosphorylation | 60/2311 | 281/18723 | 1.33e-05 | 2.68e-04 | 60 |
| GO:00071786 | Cervix | CC | transmembrane receptor protein serine/threonine kinase signaling pathway | 67/2311 | 355/18723 | 2.39e-04 | 2.67e-03 | 67 |
| GO:00163117 | Cervix | CC | dephosphorylation | 73/2311 | 417/18723 | 1.23e-03 | 9.87e-03 | 73 |
| GO:000647017 | Esophagus | HGIN | protein dephosphorylation | 61/2587 | 281/18723 | 1.86e-04 | 3.51e-03 | 61 |
| GO:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
| GO:00066433 | Esophagus | ESCC | membrane lipid metabolic process | 130/8552 | 203/18723 | 9.29e-08 | 1.54e-06 | 130 |
| GO:00464673 | Esophagus | ESCC | membrane lipid biosynthetic process | 91/8552 | 142/18723 | 7.19e-06 | 7.19e-05 | 91 |
| GO:00066652 | Esophagus | ESCC | sphingolipid metabolic process | 96/8552 | 155/18723 | 3.21e-05 | 2.66e-04 | 96 |
| GO:000717810 | Esophagus | ESCC | transmembrane receptor protein serine/threonine kinase signaling pathway | 195/8552 | 355/18723 | 2.58e-04 | 1.58e-03 | 195 |
| GO:00301481 | Esophagus | ESCC | sphingolipid biosynthetic process | 62/8552 | 103/18723 | 2.10e-03 | 9.38e-03 | 62 |
| GO:00163115 | Liver | NAFLD | dephosphorylation | 69/1882 | 417/18723 | 2.27e-05 | 6.23e-04 | 69 |
| GO:00064706 | Liver | NAFLD | protein dephosphorylation | 50/1882 | 281/18723 | 4.53e-05 | 1.09e-03 | 50 |
| GO:00071784 | Liver | NAFLD | transmembrane receptor protein serine/threonine kinase signaling pathway | 56/1882 | 355/18723 | 4.50e-04 | 6.62e-03 | 56 |
| GO:000647011 | Liver | Cirrhotic | protein dephosphorylation | 96/4634 | 281/18723 | 2.32e-04 | 2.11e-03 | 96 |
| GO:001631111 | Liver | Cirrhotic | dephosphorylation | 130/4634 | 417/18723 | 1.58e-03 | 1.03e-02 | 130 |
| GO:0006643 | Liver | Cirrhotic | membrane lipid metabolic process | 69/4634 | 203/18723 | 1.89e-03 | 1.19e-02 | 69 |
| GO:000717811 | Liver | Cirrhotic | transmembrane receptor protein serine/threonine kinase signaling pathway | 111/4634 | 355/18723 | 2.98e-03 | 1.70e-02 | 111 |
| GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
| GO:000647021 | Liver | HCC | protein dephosphorylation | 162/7958 | 281/18723 | 1.91e-07 | 3.46e-06 | 162 |
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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 |
| PPM1L | SNV | Missense_Mutation | c.689N>C | p.Asp230Ala | p.D230A | Q5SGD2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A0H0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| PPM1L | SNV | Missense_Mutation | novel | c.776G>A | p.Gly259Glu | p.G259E | Q5SGD2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR |
| PPM1L | insertion | In_Frame_Ins | novel | c.172_173insGCC | p.Met58delinsSerLeu | p.M58delinsSL | Q5SGD2 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| PPM1L | insertion | In_Frame_Ins | novel | c.173_174insCTGCTCGCGCTGCCTGCTCGGAGCCGCTTGCTC | p.Met58delinsIleCysSerArgCysLeuLeuGlyAlaAlaCysSer | p.M58delinsICSRCLLGAACS | Q5SGD2 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| PPM1L | insertion | Nonsense_Mutation | novel | c.899_900insCACGGTGTTAAGTTAAAAACCAATGCCCTCCCCCATATGT | p.Ser301ThrfsTer5 | p.S301Tfs*5 | Q5SGD2 | protein_coding | TCGA-AN-A03X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PPM1L | SNV | Missense_Mutation | rs757453078 | c.670G>A | p.Ala224Thr | p.A224T | Q5SGD2 | protein_coding | tolerated(0.12) | possibly_damaging(0.804) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PPM1L | SNV | Missense_Mutation | c.980G>T | p.Gly327Val | p.G327V | Q5SGD2 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AA-3844-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | capecitabine | PD | |
| PPM1L | SNV | Missense_Mutation | c.469N>T | p.Asp157Tyr | p.D157Y | Q5SGD2 | protein_coding | deleterious(0.02) | benign(0.203) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| PPM1L | SNV | Missense_Mutation | c.956N>C | p.Glu319Ala | p.E319A | Q5SGD2 | protein_coding | deleterious(0.01) | probably_damaging(0.935) | TCGA-AY-6196-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
| PPM1L | SNV | Missense_Mutation | novel | c.791N>A | p.Ser264Tyr | p.S264Y | Q5SGD2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | 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 |
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