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Gene: PMEL |
Gene summary for PMEL |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PMEL | Gene ID | 6490 |
| Gene name | premelanosome protein | |
| Gene Alias | D12S53E | |
| Cytomap | 12q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0006582 | UniProtAcc | P40967 |
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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 |
| 6490 | PMEL | P3_S6_AK | Human | Skin | AK | 8.33e-16 | 6.10e-01 | -0.3256 |
| 6490 | PMEL | P1_cSCC | Human | Skin | cSCC | 1.50e-03 | 2.20e-01 | 0.0292 |
| 6490 | PMEL | P4_cSCC | Human | Skin | cSCC | 3.57e-09 | 6.32e-01 | -0.00290000000000005 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:001605010 | Skin | AK | vesicle organization | 45/1910 | 300/18723 | 5.44e-03 | 3.02e-02 | 45 |
| GO:001605015 | Skin | cSCC | vesicle organization | 135/4864 | 300/18723 | 5.98e-13 | 3.44e-11 | 135 |
| GO:00324382 | Skin | cSCC | melanosome organization | 14/4864 | 28/18723 | 5.47e-03 | 2.73e-02 | 14 |
| GO:00487532 | Skin | cSCC | pigment granule organization | 14/4864 | 29/18723 | 8.08e-03 | 3.74e-02 | 14 |
| GO:00330594 | Skin | cSCC | cellular pigmentation | 22/4864 | 53/18723 | 9.80e-03 | 4.33e-02 | 22 |
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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 |
| PMEL | SNV | Missense_Mutation | novel | c.209T>C | p.Val70Ala | p.V70A | P40967 | protein_coding | deleterious(0) | possibly_damaging(0.475) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| PMEL | SNV | Missense_Mutation | c.701N>T | p.Arg234Ile | p.R234I | P40967 | protein_coding | deleterious(0) | possibly_damaging(0.809) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PMEL | insertion | Frame_Shift_Ins | novel | c.548_549insAC | p.Met184ProfsTer4 | p.M184Pfs*4 | P40967 | protein_coding | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
| PMEL | SNV | Missense_Mutation | rs199615476 | c.1555N>A | p.Gly519Arg | p.G519R | P40967 | protein_coding | tolerated(0.07) | benign(0.381) | TCGA-A5-A2K3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD |
| PMEL | SNV | Missense_Mutation | novel | c.1318N>T | p.Asp440Tyr | p.D440Y | P40967 | protein_coding | deleterious(0.01) | possibly_damaging(0.8) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| PMEL | SNV | Missense_Mutation | novel | c.282N>C | p.Gln94His | p.Q94H | P40967 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| PMEL | SNV | Missense_Mutation | novel | c.1243N>A | p.Ala415Thr | p.A415T | P40967 | protein_coding | tolerated(0.28) | benign(0.013) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PMEL | SNV | Missense_Mutation | rs778118794 | c.1900N>A | p.Val634Ile | p.V634I | P40967 | protein_coding | tolerated(0.37) | benign(0.001) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PMEL | SNV | Missense_Mutation | novel | c.1117N>A | p.Gly373Ser | p.G373S | P40967 | protein_coding | tolerated(0.2) | benign(0.023) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PMEL | SNV | Missense_Mutation | rs746019205 | c.1874G>A | p.Arg625His | p.R625H | P40967 | protein_coding | tolerated(0.11) | benign(0.009) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | 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 |
| 6490 | PMEL | DRUGGABLE GENOME | Multi-epitope tyrosinase/gp100 vaccine | |||
| 6490 | PMEL | DRUGGABLE GENOME | Melanoma vaccine | |||
| 6490 | PMEL | DRUGGABLE GENOME | HMBA | 11310793 | ||
| 6490 | PMEL | DRUGGABLE GENOME | GPA-TriMAR-T cells | |||
| 6490 | PMEL | DRUGGABLE GENOME | Multi-epitope peptide melanoma vaccine | 22495394 | ||
| 6490 | PMEL | DRUGGABLE GENOME | AE-08 | |||
| 6490 | PMEL | DRUGGABLE GENOME | IMCgp100 | TEBENTAFUSP | 23263452 | |
| 6490 | PMEL | DRUGGABLE GENOME | Gp100:209-217(210M) peptide vaccine | |||
| 6490 | PMEL | DRUGGABLE GENOME | IFN | 15980237 |
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