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Gene: PCMT1 |
Gene summary for PCMT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PCMT1 | Gene ID | 5110 |
| Gene name | protein-L-isoaspartate (D-aspartate) O-methyltransferase | |
| Gene Alias | PIMT | |
| Cytomap | 6q25.1 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | H7BY58 |
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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 |
| 5110 | PCMT1 | NCCBC14 | Human | Breast | DCIS | 1.34e-08 | -1.66e-01 | 0.2021 |
| 5110 | PCMT1 | NCCBC2 | Human | Breast | DCIS | 1.50e-04 | -5.15e-02 | 0.1554 |
| 5110 | PCMT1 | NCCBC5 | Human | Breast | DCIS | 4.44e-08 | -4.69e-02 | 0.2046 |
| 5110 | PCMT1 | P1 | Human | Breast | IDC | 4.54e-09 | -7.99e-02 | 0.1527 |
| 5110 | PCMT1 | DCIS2 | Human | Breast | DCIS | 1.41e-60 | 2.01e-01 | 0.0085 |
| 5110 | PCMT1 | LZE2T | Human | Esophagus | ESCC | 6.50e-03 | 3.53e-01 | 0.082 |
| 5110 | PCMT1 | LZE4T | Human | Esophagus | ESCC | 3.02e-20 | 6.36e-01 | 0.0811 |
| 5110 | PCMT1 | LZE7T | Human | Esophagus | ESCC | 3.13e-04 | 7.32e-01 | 0.0667 |
| 5110 | PCMT1 | LZE8T | Human | Esophagus | ESCC | 2.41e-05 | 3.11e-01 | 0.067 |
| 5110 | PCMT1 | LZE22T | Human | Esophagus | ESCC | 2.03e-03 | 6.30e-01 | 0.068 |
| 5110 | PCMT1 | LZE24T | Human | Esophagus | ESCC | 5.24e-20 | 5.29e-01 | 0.0596 |
| 5110 | PCMT1 | LZE6T | Human | Esophagus | ESCC | 8.79e-04 | 6.26e-01 | 0.0845 |
| 5110 | PCMT1 | P1T-E | Human | Esophagus | ESCC | 2.33e-07 | 2.71e-01 | 0.0875 |
| 5110 | PCMT1 | P2T-E | Human | Esophagus | ESCC | 3.66e-40 | 7.53e-01 | 0.1177 |
| 5110 | PCMT1 | P4T-E | Human | Esophagus | ESCC | 4.82e-37 | 1.07e+00 | 0.1323 |
| 5110 | PCMT1 | P5T-E | Human | Esophagus | ESCC | 2.20e-38 | 9.19e-01 | 0.1327 |
| 5110 | PCMT1 | P8T-E | Human | Esophagus | ESCC | 3.68e-30 | 6.90e-01 | 0.0889 |
| 5110 | PCMT1 | P9T-E | Human | Esophagus | ESCC | 2.53e-10 | 4.21e-01 | 0.1131 |
| 5110 | PCMT1 | P10T-E | Human | Esophagus | ESCC | 2.39e-39 | 7.18e-01 | 0.116 |
| 5110 | PCMT1 | P11T-E | Human | Esophagus | ESCC | 3.68e-23 | 1.20e+00 | 0.1426 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
| GO:000647914 | Esophagus | ESCC | protein methylation | 115/8552 | 181/18723 | 9.07e-07 | 1.16e-05 | 115 |
| GO:000821314 | Esophagus | ESCC | protein alkylation | 115/8552 | 181/18723 | 9.07e-07 | 1.16e-05 | 115 |
| GO:00064791 | Liver | Cirrhotic | protein methylation | 61/4634 | 181/18723 | 4.13e-03 | 2.21e-02 | 61 |
| GO:00082131 | Liver | Cirrhotic | protein alkylation | 61/4634 | 181/18723 | 4.13e-03 | 2.21e-02 | 61 |
| GO:00434141 | Liver | HCC | macromolecule methylation | 183/7958 | 316/18723 | 2.00e-08 | 4.72e-07 | 183 |
| GO:0032259 | Liver | HCC | methylation | 206/7958 | 364/18723 | 3.35e-08 | 7.53e-07 | 206 |
| GO:00064792 | Liver | HCC | protein methylation | 111/7958 | 181/18723 | 2.36e-07 | 4.18e-06 | 111 |
| GO:00082132 | Liver | HCC | protein alkylation | 111/7958 | 181/18723 | 2.36e-07 | 4.18e-06 | 111 |
| GO:00064797 | Oral cavity | OSCC | protein methylation | 92/7305 | 181/18723 | 7.86e-04 | 4.26e-03 | 92 |
| GO:00082137 | Oral cavity | OSCC | protein alkylation | 92/7305 | 181/18723 | 7.86e-04 | 4.26e-03 | 92 |
| GO:00434142 | Oral cavity | OSCC | macromolecule methylation | 149/7305 | 316/18723 | 1.82e-03 | 8.60e-03 | 149 |
| GO:00322591 | Oral cavity | OSCC | methylation | 168/7305 | 364/18723 | 3.03e-03 | 1.31e-02 | 168 |
| GO:000647915 | Skin | cSCC | protein methylation | 67/4864 | 181/18723 | 6.65e-04 | 4.75e-03 | 67 |
| GO:000821315 | Skin | cSCC | protein alkylation | 67/4864 | 181/18723 | 6.65e-04 | 4.75e-03 | 67 |
| GO:004341411 | Skin | cSCC | macromolecule methylation | 107/4864 | 316/18723 | 1.03e-03 | 6.94e-03 | 107 |
| GO:00322593 | Skin | cSCC | methylation | 120/4864 | 364/18723 | 1.61e-03 | 9.93e-03 | 120 |
| GO:000647910 | Thyroid | PTC | protein methylation | 82/5968 | 181/18723 | 1.01e-04 | 8.21e-04 | 82 |
| GO:000821310 | Thyroid | PTC | protein alkylation | 82/5968 | 181/18723 | 1.01e-04 | 8.21e-04 | 82 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| PCMT1 | SNV | Missense_Mutation | c.256G>C | p.Val86Leu | p.V86L | protein_coding | deleterious(0) | possibly_damaging(0.826) | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| PCMT1 | SNV | Missense_Mutation | c.188N>T | p.Ser63Phe | p.S63F | protein_coding | tolerated(0.08) | probably_damaging(0.979) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PCMT1 | deletion | Frame_Shift_Del | novel | c.801delN | p.Val269Ter | p.V269* | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
| PCMT1 | SNV | Missense_Mutation | rs754551183 | c.200G>A | p.Ser67Asn | p.S67N | protein_coding | tolerated(0.5) | benign(0.001) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| PCMT1 | SNV | Missense_Mutation | novel | c.291N>A | p.His97Gln | p.H97Q | protein_coding | tolerated(0.07) | possibly_damaging(0.698) | TCGA-A6-3808-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PCMT1 | SNV | Missense_Mutation | novel | c.481N>C | p.Thr161Pro | p.T161P | protein_coding | tolerated(0.09) | benign(0.324) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PCMT1 | SNV | Missense_Mutation | novel | c.718N>T | p.Pro240Ser | p.P240S | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-F4-6808-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PCMT1 | SNV | Missense_Mutation | rs769452465 | c.677N>T | p.Ala226Val | p.A226V | protein_coding | deleterious(0.03) | possibly_damaging(0.907) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PCMT1 | SNV | Missense_Mutation | novel | c.419N>T | p.Ala140Val | p.A140V | protein_coding | tolerated(0.32) | benign(0.239) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD | |
| PCMT1 | SNV | Missense_Mutation | novel | c.611N>A | p.Gly204Glu | p.G204E | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | 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 |
| Page: 1 |
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