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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 | c.1193C>A | p.Thr398Lys | p.T398K | P40967 | protein_coding | tolerated(0.93) | benign(0.003) | TCGA-A2-A25D-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| PMEL | SNV | Missense_Mutation | c.493N>A | p.Gly165Ser | p.G165S | P40967 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-BH-A203-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PMEL | SNV | Missense_Mutation | c.884C>G | p.Ala295Gly | p.A295G | P40967 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PMEL | SNV | Missense_Mutation | c.444N>A | p.Ser148Arg | p.S148R | P40967 | protein_coding | tolerated(0.84) | benign(0.014) | TCGA-D8-A1JP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| PMEL | SNV | Missense_Mutation | rs753939918 | c.814N>T | p.Arg272Trp | p.R272W | P40967 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-OL-A5RW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| PMEL | SNV | Missense_Mutation | novel | c.991N>A | p.Glu331Lys | p.E331K | P40967 | protein_coding | tolerated(0.65) | benign(0.009) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PMEL | SNV | Missense_Mutation | c.1181C>T | p.Thr394Ile | p.T394I | P40967 | protein_coding | deleterious(0.01) | possibly_damaging(0.859) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PMEL | SNV | Missense_Mutation | rs866948103 | c.1946G>A | p.Arg649His | p.R649H | P40967 | protein_coding | tolerated(0.09) | benign(0.003) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PMEL | SNV | Missense_Mutation | c.101N>T | p.Gly34Val | p.G34V | P40967 | protein_coding | deleterious(0) | possibly_damaging(0.817) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PMEL | SNV | Missense_Mutation | c.1159N>G | p.Thr387Ala | p.T387A | P40967 | protein_coding | tolerated(0.26) | probably_damaging(0.995) | TCGA-AG-4015-01 | Colorectum | rectum adenocarcinoma | Female | >=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 |
| 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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