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Gene: XRCC4 |
Gene summary for XRCC4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | XRCC4 | Gene ID | 7518 |
| Gene name | X-ray repair cross complementing 4 | |
| Gene Alias | SSMED | |
| Cytomap | 5q14.2 | |
| Gene Type | protein-coding | GO ID | GO:0002200 | UniProtAcc | A0A024RAQ8 |
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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 |
| 7518 | XRCC4 | LZE24T | Human | Esophagus | ESCC | 2.72e-09 | 2.04e-01 | 0.0596 |
| 7518 | XRCC4 | P1T-E | Human | Esophagus | ESCC | 1.25e-03 | 1.81e-01 | 0.0875 |
| 7518 | XRCC4 | P2T-E | Human | Esophagus | ESCC | 8.13e-11 | 1.86e-01 | 0.1177 |
| 7518 | XRCC4 | P4T-E | Human | Esophagus | ESCC | 6.63e-06 | 1.54e-01 | 0.1323 |
| 7518 | XRCC4 | P5T-E | Human | Esophagus | ESCC | 7.94e-03 | 1.05e-01 | 0.1327 |
| 7518 | XRCC4 | P8T-E | Human | Esophagus | ESCC | 7.46e-13 | 1.18e-01 | 0.0889 |
| 7518 | XRCC4 | P9T-E | Human | Esophagus | ESCC | 1.30e-03 | 1.67e-01 | 0.1131 |
| 7518 | XRCC4 | P10T-E | Human | Esophagus | ESCC | 4.04e-04 | 8.56e-02 | 0.116 |
| 7518 | XRCC4 | P11T-E | Human | Esophagus | ESCC | 1.00e-03 | 1.55e-01 | 0.1426 |
| 7518 | XRCC4 | P12T-E | Human | Esophagus | ESCC | 6.72e-10 | 1.38e-01 | 0.1122 |
| 7518 | XRCC4 | P20T-E | Human | Esophagus | ESCC | 6.58e-06 | 1.49e-01 | 0.1124 |
| 7518 | XRCC4 | P21T-E | Human | Esophagus | ESCC | 5.41e-10 | 1.36e-01 | 0.1617 |
| 7518 | XRCC4 | P22T-E | Human | Esophagus | ESCC | 1.78e-04 | 1.06e-01 | 0.1236 |
| 7518 | XRCC4 | P24T-E | Human | Esophagus | ESCC | 1.66e-05 | 2.11e-01 | 0.1287 |
| 7518 | XRCC4 | P26T-E | Human | Esophagus | ESCC | 1.93e-04 | 1.14e-01 | 0.1276 |
| 7518 | XRCC4 | P31T-E | Human | Esophagus | ESCC | 1.25e-10 | 2.38e-01 | 0.1251 |
| 7518 | XRCC4 | P32T-E | Human | Esophagus | ESCC | 3.55e-10 | 2.75e-01 | 0.1666 |
| 7518 | XRCC4 | P36T-E | Human | Esophagus | ESCC | 3.85e-02 | 1.16e-01 | 0.1187 |
| 7518 | XRCC4 | P37T-E | Human | Esophagus | ESCC | 6.25e-06 | 1.77e-01 | 0.1371 |
| 7518 | XRCC4 | P47T-E | Human | Esophagus | ESCC | 2.09e-02 | 6.46e-02 | 0.1067 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:001021217 | Esophagus | ESCC | response to ionizing radiation | 110/8552 | 148/18723 | 1.11e-12 | 4.78e-11 | 110 |
| GO:000931419 | Esophagus | ESCC | response to radiation | 277/8552 | 456/18723 | 4.42e-11 | 1.43e-09 | 277 |
| GO:003450211 | Esophagus | ESCC | protein localization to chromosome | 70/8552 | 92/18723 | 2.54e-09 | 5.64e-08 | 70 |
| GO:00063024 | Esophagus | ESCC | double-strand break repair | 152/8552 | 251/18723 | 1.33e-06 | 1.62e-05 | 152 |
| GO:001003827 | Esophagus | ESCC | response to metal ion | 208/8552 | 373/18723 | 5.02e-05 | 3.90e-04 | 208 |
| GO:00063101 | Esophagus | ESCC | DNA recombination | 168/8552 | 305/18723 | 5.58e-04 | 3.05e-03 | 168 |
| GO:00025622 | Esophagus | ESCC | somatic diversification of immune receptors via germline recombination within a single locus | 43/8552 | 66/18723 | 1.10e-03 | 5.53e-03 | 43 |
| GO:0006303 | Esophagus | ESCC | double-strand break repair via nonhomologous end joining | 43/8552 | 66/18723 | 1.10e-03 | 5.53e-03 | 43 |
| GO:00164442 | Esophagus | ESCC | somatic cell DNA recombination | 43/8552 | 66/18723 | 1.10e-03 | 5.53e-03 | 43 |
| GO:00164472 | Esophagus | ESCC | somatic recombination of immunoglobulin gene segments | 38/8552 | 57/18723 | 1.11e-03 | 5.56e-03 | 38 |
| GO:00022003 | Esophagus | ESCC | somatic diversification of immune receptors | 49/8552 | 77/18723 | 1.12e-03 | 5.60e-03 | 49 |
| GO:00101653 | Esophagus | ESCC | response to X-ray | 24/8552 | 33/18723 | 1.50e-03 | 7.06e-03 | 24 |
| GO:00164452 | Esophagus | ESCC | somatic diversification of immunoglobulins | 43/8552 | 67/18723 | 1.73e-03 | 7.97e-03 | 43 |
| GO:007124117 | Esophagus | ESCC | cellular response to inorganic substance | 125/8552 | 226/18723 | 2.17e-03 | 9.67e-03 | 125 |
| GO:00062661 | Esophagus | ESCC | DNA ligation | 13/8552 | 16/18723 | 4.05e-03 | 1.62e-02 | 13 |
| GO:00102128 | Oral cavity | OSCC | response to ionizing radiation | 99/7305 | 148/18723 | 5.49e-12 | 2.08e-10 | 99 |
| GO:000931416 | Oral cavity | OSCC | response to radiation | 241/7305 | 456/18723 | 9.76e-10 | 2.40e-08 | 241 |
| GO:00345023 | Oral cavity | OSCC | protein localization to chromosome | 60/7305 | 92/18723 | 3.17e-07 | 4.79e-06 | 60 |
| GO:001003820 | Oral cavity | OSCC | response to metal ion | 188/7305 | 373/18723 | 4.34e-06 | 5.00e-05 | 188 |
| GO:00063023 | Oral cavity | OSCC | double-strand break repair | 132/7305 | 251/18723 | 7.93e-06 | 8.52e-05 | 132 |
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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 |
| XRCC4 | ICAF | Pancreas | PDAC | CYP26A1,HOPX,RGS16, etc. | 1.91e-01 |  |
| XRCC4 | STM | Skin | AK | FOXE1,TUBD1,AC093157.1, etc. | 1.28e-01 |  |
| XRCC4 | STM | Skin | SCCIS | FOXE1,TUBD1,AC093157.1, etc. | 3.43e-01 |  |
| ∗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 |
| XRCC4 | SNV | Missense_Mutation | c.793N>A | p.Asp265Asn | p.D265N | Q13426 | protein_coding | deleterious(0.02) | probably_damaging(0.998) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| XRCC4 | SNV | Missense_Mutation | novel | c.288N>A | p.Phe96Leu | p.F96L | Q13426 | protein_coding | deleterious(0) | benign(0.074) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| XRCC4 | SNV | Missense_Mutation | novel | c.588N>A | p.Asn196Lys | p.N196K | Q13426 | protein_coding | tolerated(0.44) | probably_damaging(0.933) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| XRCC4 | SNV | Missense_Mutation | rs527506822 | c.824G>A | p.Arg275Gln | p.R275Q | Q13426 | protein_coding | deleterious(0.02) | possibly_damaging(0.869) | TCGA-AR-A0TX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| XRCC4 | SNV | Missense_Mutation | novel | c.779N>A | p.Ser260Asn | p.S260N | Q13426 | protein_coding | tolerated(0.09) | benign(0.41) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| XRCC4 | SNV | Missense_Mutation | c.658N>C | p.Glu220Gln | p.E220Q | Q13426 | protein_coding | tolerated(0.57) | benign(0.038) | TCGA-BH-A0W7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
| XRCC4 | SNV | Missense_Mutation | rs780229187 | c.949N>A | p.Glu317Lys | p.E317K | Q13426 | protein_coding | tolerated(0.24) | benign(0.144) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| XRCC4 | SNV | Missense_Mutation | c.688N>A | p.Asp230Asn | p.D230N | Q13426 | protein_coding | tolerated(0.14) | possibly_damaging(0.647) | TCGA-E9-A1NA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| XRCC4 | SNV | Missense_Mutation | novel | c.72G>T | p.Trp24Cys | p.W24C | Q13426 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| XRCC4 | SNV | Missense_Mutation | c.908N>A | p.Ser303Tyr | p.S303Y | Q13426 | protein_coding | deleterious(0.02) | possibly_damaging(0.887) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=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 |
| 7518 | XRCC4 | KINASE | fluorouracil | FLUOROURACIL | 28796378 | |
| 7518 | XRCC4 | KINASE | docetaxel | DOCETAXEL | 20157331 | |
| 7518 | XRCC4 | KINASE | radiotherapy | 28796378 | ||
| 7518 | XRCC4 | KINASE | Platinum compounds | 28796378 |
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