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Gene: R3HDM1 |
Gene summary for R3HDM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | R3HDM1 | Gene ID | 23518 |
| Gene name | R3H domain containing 1 | |
| Gene Alias | R3HDM | |
| Cytomap | 2q21.3 | |
| Gene Type | protein-coding | GO ID | GO:0003674 | UniProtAcc | Q15032 |
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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 |
| 23518 | R3HDM1 | CCI_1 | Human | Cervix | CC | 5.26e-05 | 7.99e-01 | 0.528 |
| 23518 | R3HDM1 | CCI_2 | Human | Cervix | CC | 2.05e-07 | 9.88e-01 | 0.5249 |
| 23518 | R3HDM1 | CCI_3 | Human | Cervix | CC | 2.03e-12 | 8.49e-01 | 0.516 |
| 23518 | R3HDM1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.21e-08 | -2.90e-01 | 0.0155 |
| 23518 | R3HDM1 | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.77e-02 | -6.75e-01 | -0.1462 |
| 23518 | R3HDM1 | F007 | Human | Colorectum | FAP | 1.38e-03 | -3.64e-01 | 0.1176 |
| 23518 | R3HDM1 | A001-C-207 | Human | Colorectum | FAP | 1.56e-06 | -3.75e-01 | 0.1278 |
| 23518 | R3HDM1 | A015-C-203 | Human | Colorectum | FAP | 5.43e-38 | -6.11e-01 | -0.1294 |
| 23518 | R3HDM1 | A015-C-204 | Human | Colorectum | FAP | 8.94e-08 | -3.48e-01 | -0.0228 |
| 23518 | R3HDM1 | A014-C-040 | Human | Colorectum | FAP | 4.44e-06 | -5.33e-01 | -0.1184 |
| 23518 | R3HDM1 | A002-C-201 | Human | Colorectum | FAP | 1.27e-16 | -4.45e-01 | 0.0324 |
| 23518 | R3HDM1 | A001-C-119 | Human | Colorectum | FAP | 1.39e-11 | -5.31e-01 | -0.1557 |
| 23518 | R3HDM1 | A001-C-108 | Human | Colorectum | FAP | 5.43e-20 | -4.46e-01 | -0.0272 |
| 23518 | R3HDM1 | A002-C-205 | Human | Colorectum | FAP | 4.29e-23 | -4.46e-01 | -0.1236 |
| 23518 | R3HDM1 | A014-C-108 | Human | Colorectum | FAP | 1.82e-02 | -3.50e-01 | -0.124 |
| 23518 | R3HDM1 | A001-C-104 | Human | Colorectum | FAP | 4.58e-09 | -3.71e-01 | 0.0184 |
| 23518 | R3HDM1 | A015-C-005 | Human | Colorectum | FAP | 1.76e-07 | -3.36e-01 | -0.0336 |
| 23518 | R3HDM1 | A015-C-006 | Human | Colorectum | FAP | 3.20e-16 | -5.46e-01 | -0.0994 |
| 23518 | R3HDM1 | A015-C-106 | Human | Colorectum | FAP | 9.51e-19 | -3.87e-01 | -0.0511 |
| 23518 | R3HDM1 | A002-C-114 | Human | Colorectum | FAP | 3.65e-22 | -5.63e-01 | -0.1561 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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 |
| Page: 1 |
| 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 |
| R3HDM1 | SNV | Missense_Mutation | novel | c.1205N>T | p.Arg402Met | p.R402M | Q15032 | protein_coding | deleterious(0) | probably_damaging(0.942) | TCGA-NJ-A4YQ-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| R3HDM1 | SNV | Missense_Mutation | novel | c.1366N>C | p.Asp456His | p.D456H | Q15032 | protein_coding | deleterious(0.02) | possibly_damaging(0.846) | TCGA-21-1082-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| R3HDM1 | SNV | Missense_Mutation | c.1726N>T | p.Leu576Phe | p.L576F | Q15032 | protein_coding | tolerated(0.25) | possibly_damaging(0.448) | TCGA-21-5784-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| R3HDM1 | SNV | Missense_Mutation | c.1447N>T | p.Gly483Cys | p.G483C | Q15032 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-22-4613-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| R3HDM1 | SNV | Missense_Mutation | novel | c.70N>G | p.Lys24Glu | p.K24E | Q15032 | protein_coding | tolerated(0.74) | benign(0.049) | TCGA-33-AASB-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| R3HDM1 | SNV | Missense_Mutation | novel | c.2657N>G | p.Pro886Arg | p.P886R | Q15032 | protein_coding | deleterious(0) | probably_damaging(0.929) | TCGA-34-2609-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | gemcitabine | PD |
| R3HDM1 | SNV | Missense_Mutation | novel | c.2221G>A | p.Gly741Ser | p.G741S | Q15032 | protein_coding | tolerated(0.05) | benign(0.249) | TCGA-43-7658-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| R3HDM1 | SNV | Missense_Mutation | novel | c.130N>C | p.Glu44Gln | p.E44Q | Q15032 | protein_coding | deleterious(0) | benign(0.107) | TCGA-56-A5DR-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| R3HDM1 | SNV | Missense_Mutation | novel | c.498N>T | p.Arg166Ser | p.R166S | Q15032 | protein_coding | deleterious(0.01) | benign(0.399) | TCGA-56-A62T-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | CR |
| R3HDM1 | SNV | Missense_Mutation | c.773G>C | p.Arg258Thr | p.R258T | Q15032 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-60-2698-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | mithramycin | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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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