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Gene: RDH16 |
Gene summary for RDH16 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RDH16 | Gene ID | 8608 |
| Gene name | retinol dehydrogenase 16 | |
| Gene Alias | RODH-4 | |
| Cytomap | 12q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0001523 | UniProtAcc | Q59FX7 |
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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 |
| 8608 | RDH16 | C04 | Human | Oral cavity | OSCC | 3.41e-02 | 1.50e-01 | 0.2633 |
| 8608 | RDH16 | C21 | Human | Oral cavity | OSCC | 2.04e-04 | 1.97e-01 | 0.2678 |
| 8608 | RDH16 | C30 | Human | Oral cavity | OSCC | 5.33e-08 | 3.79e-01 | 0.3055 |
| 8608 | RDH16 | C38 | Human | Oral cavity | OSCC | 3.61e-03 | 3.84e-01 | 0.172 |
| 8608 | RDH16 | C43 | Human | Oral cavity | OSCC | 5.27e-33 | 5.59e-01 | 0.1704 |
| 8608 | RDH16 | C46 | Human | Oral cavity | OSCC | 1.64e-03 | 1.36e-01 | 0.1673 |
| 8608 | RDH16 | C51 | Human | Oral cavity | OSCC | 8.80e-22 | 9.01e-01 | 0.2674 |
| 8608 | RDH16 | C06 | Human | Oral cavity | OSCC | 2.90e-05 | 5.35e-01 | 0.2699 |
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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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:002290018 | Oral cavity | OSCC | electron transport chain | 126/7305 | 175/18723 | 6.65e-19 | 8.42e-17 | 126 |
| GO:000609118 | Oral cavity | OSCC | generation of precursor metabolites and energy | 286/7305 | 490/18723 | 1.45e-18 | 1.71e-16 | 286 |
| GO:00060667 | Oral cavity | OSCC | alcohol metabolic process | 179/7305 | 353/18723 | 4.54e-06 | 5.21e-05 | 179 |
| GO:00067203 | Oral cavity | OSCC | isoprenoid metabolic process | 59/7305 | 116/18723 | 6.18e-03 | 2.33e-02 | 59 |
| GO:00082024 | Oral cavity | OSCC | steroid metabolic process | 146/7305 | 319/18723 | 7.78e-03 | 2.85e-02 | 146 |
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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 |
| RDH16 | insertion | Nonsense_Mutation | novel | c.40_41insACTAATTCATCTGTCTTATTATAGAGGAAGAAAGAAACATGGAT | p.Leu14HisfsTer2 | p.L14Hfs*2 | O75452 | protein_coding | TCGA-A2-A0EX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RDH16 | SNV | Missense_Mutation | c.833G>A | p.Arg278His | p.R278H | O75452 | protein_coding | tolerated(0.06) | benign(0.082) | TCGA-JW-AAVH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RDH16 | SNV | Missense_Mutation | novel | c.329N>C | p.Val110Ala | p.V110A | O75452 | protein_coding | deleterious(0.01) | possibly_damaging(0.901) | TCGA-MA-AA42-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| RDH16 | SNV | Missense_Mutation | rs745990933 | c.839N>A | p.Arg280His | p.R280H | O75452 | protein_coding | deleterious(0.03) | possibly_damaging(0.468) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| RDH16 | SNV | Missense_Mutation | c.790N>A | p.Val264Met | p.V264M | O75452 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| RDH16 | SNV | Missense_Mutation | c.815T>G | p.Leu272Arg | p.L272R | O75452 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AA-A01P-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| RDH16 | SNV | Missense_Mutation | rs762842316 | c.686N>A | p.Arg229Gln | p.R229Q | O75452 | protein_coding | tolerated(0.53) | benign(0.006) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RDH16 | SNV | Missense_Mutation | rs200529763 | c.770G>A | p.Cys257Tyr | p.C257Y | O75452 | protein_coding | tolerated(0.13) | benign(0.009) | TCGA-G4-6299-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Ancillary | leucovorin | SD |
| RDH16 | SNV | Missense_Mutation | novel | c.431T>G | p.Val144Gly | p.V144G | O75452 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AG-A02X-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RDH16 | deletion | Frame_Shift_Del | rs755216247 | c.832delC | p.Arg278ValfsTer17 | p.R278Vfs*17 | O75452 | protein_coding | TCGA-AA-3492-01 | Colorectum | colon 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 |
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