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Gene: XRCC6 |
Gene summary for XRCC6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | XRCC6 | Gene ID | 2547 |
| Gene name | X-ray repair cross complementing 6 | |
| Gene Alias | CTC75 | |
| Cytomap | 22q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000723 | UniProtAcc | A0A024R1N4 |
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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 |
| 2547 | XRCC6 | HTA11_3410_2000001011 | Human | Colorectum | AD | 8.53e-16 | 4.29e-01 | 0.0155 |
| 2547 | XRCC6 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.44e-12 | 6.64e-01 | -0.1808 |
| 2547 | XRCC6 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.19e-20 | 9.71e-01 | -0.0811 |
| 2547 | XRCC6 | HTA11_78_2000001011 | Human | Colorectum | AD | 5.08e-08 | 5.19e-01 | -0.1088 |
| 2547 | XRCC6 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.52e-25 | 7.70e-01 | -0.1954 |
| 2547 | XRCC6 | HTA11_411_2000001011 | Human | Colorectum | SER | 3.78e-07 | 1.06e+00 | -0.2602 |
| 2547 | XRCC6 | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.08e-04 | 8.22e-01 | -0.2196 |
| 2547 | XRCC6 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.24e-14 | 8.11e-01 | -0.1207 |
| 2547 | XRCC6 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.74e-10 | 8.30e-01 | -0.1526 |
| 2547 | XRCC6 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.39e-32 | 9.71e-01 | -0.1464 |
| 2547 | XRCC6 | HTA11_866_2000001011 | Human | Colorectum | AD | 5.86e-09 | 5.09e-01 | -0.1001 |
| 2547 | XRCC6 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.01e-30 | 1.23e+00 | -0.059 |
| 2547 | XRCC6 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.64e-07 | 8.84e-01 | -0.1706 |
| 2547 | XRCC6 | HTA11_5212_2000001011 | Human | Colorectum | AD | 9.94e-08 | 6.16e-01 | -0.2061 |
| 2547 | XRCC6 | HTA11_5216_2000001011 | Human | Colorectum | SER | 7.26e-06 | 7.62e-01 | -0.1462 |
| 2547 | XRCC6 | HTA11_546_2000001011 | Human | Colorectum | AD | 2.14e-12 | 7.98e-01 | -0.0842 |
| 2547 | XRCC6 | HTA11_7862_2000001011 | Human | Colorectum | AD | 2.08e-02 | 4.53e-01 | -0.0179 |
| 2547 | XRCC6 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.95e-31 | 9.72e-01 | 0.096 |
| 2547 | XRCC6 | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.23e-07 | 9.03e-01 | 0.0446 |
| 2547 | XRCC6 | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.59e-07 | 6.70e-01 | 0.0528 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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 |
| GO:0062197 | Colorectum | AD | cellular response to chemical stress | 109/3918 | 337/18723 | 5.33e-07 | 1.95e-05 | 109 |
| GO:0033674 | Colorectum | AD | positive regulation of kinase activity | 131/3918 | 467/18723 | 1.28e-04 | 1.85e-03 | 131 |
| GO:0045860 | Colorectum | AD | positive regulation of protein kinase activity | 107/3918 | 386/18723 | 8.01e-04 | 7.92e-03 | 107 |
| GO:0000723 | Colorectum | AD | telomere maintenance | 43/3918 | 131/18723 | 9.77e-04 | 9.20e-03 | 43 |
| GO:0032392 | Colorectum | AD | DNA geometric change | 31/3918 | 90/18723 | 2.02e-03 | 1.63e-02 | 31 |
| GO:1903706 | Colorectum | AD | regulation of hemopoiesis | 99/3918 | 367/18723 | 3.08e-03 | 2.28e-02 | 99 |
| GO:0071481 | Colorectum | AD | cellular response to X-ray | 8/3918 | 14/18723 | 3.23e-03 | 2.38e-02 | 8 |
| GO:0071472 | Colorectum | AD | cellular response to salt stress | 7/3918 | 12/18723 | 5.09e-03 | 3.38e-02 | 7 |
| GO:00621971 | Colorectum | SER | cellular response to chemical stress | 87/2897 | 337/18723 | 5.33e-07 | 2.59e-05 | 87 |
| GO:00336741 | Colorectum | SER | positive regulation of kinase activity | 95/2897 | 467/18723 | 2.62e-03 | 2.41e-02 | 95 |
| GO:00714811 | Colorectum | SER | cellular response to X-ray | 7/2897 | 14/18723 | 2.64e-03 | 2.41e-02 | 7 |
| GO:0006970 | Colorectum | SER | response to osmotic stress | 23/2897 | 84/18723 | 3.61e-03 | 3.03e-02 | 23 |
| GO:00458601 | Colorectum | SER | positive regulation of protein kinase activity | 79/2897 | 386/18723 | 4.85e-03 | 3.79e-02 | 79 |
| GO:00007231 | Colorectum | SER | telomere maintenance | 32/2897 | 131/18723 | 4.90e-03 | 3.82e-02 | 32 |
| GO:00714721 | Colorectum | SER | cellular response to salt stress | 6/2897 | 12/18723 | 5.42e-03 | 4.03e-02 | 6 |
| GO:00621972 | Colorectum | MSS | cellular response to chemical stress | 102/3467 | 337/18723 | 9.73e-08 | 4.71e-06 | 102 |
| GO:00336742 | Colorectum | MSS | positive regulation of kinase activity | 122/3467 | 467/18723 | 2.50e-05 | 5.21e-04 | 122 |
| GO:00458602 | Colorectum | MSS | positive regulation of protein kinase activity | 102/3467 | 386/18723 | 6.93e-05 | 1.20e-03 | 102 |
| GO:00007232 | Colorectum | MSS | telomere maintenance | 40/3467 | 131/18723 | 5.86e-04 | 6.49e-03 | 40 |
| GO:00323921 | Colorectum | MSS | DNA geometric change | 29/3467 | 90/18723 | 1.26e-03 | 1.20e-02 | 29 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 |
| 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 |
| XRCC6 | SNV | Missense_Mutation | rs765303000 | c.344G>A | p.Arg115Gln | p.R115Q | P12956 | protein_coding | tolerated(0.15) | benign(0.121) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| XRCC6 | SNV | Missense_Mutation | c.31N>C | p.Glu11Gln | p.E11Q | P12956 | protein_coding | tolerated(0.1) | benign(0.043) | TCGA-C8-A12Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| XRCC6 | SNV | Missense_Mutation | c.160N>A | p.Glu54Lys | p.E54K | P12956 | protein_coding | deleterious(0.04) | benign(0.127) | TCGA-C8-A12Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| XRCC6 | SNV | Missense_Mutation | c.492N>C | p.Lys164Asn | p.K164N | P12956 | protein_coding | deleterious(0) | probably_damaging(0.923) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR | |
| XRCC6 | SNV | Missense_Mutation | c.882A>T | p.Glu294Asp | p.E294D | P12956 | protein_coding | deleterious(0.02) | possibly_damaging(0.677) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| XRCC6 | SNV | Missense_Mutation | c.1715N>T | p.Thr572Met | p.T572M | P12956 | protein_coding | deleterious(0.03) | benign(0.194) | TCGA-E9-A22H-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| XRCC6 | SNV | Missense_Mutation | novel | c.535N>C | p.Asp179His | p.D179H | P12956 | protein_coding | deleterious(0) | probably_damaging(0.938) | TCGA-JL-A3YW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| XRCC6 | insertion | Nonsense_Mutation | novel | c.1675_1676insGGCGCCTGTAGTCCCAACTACCTGGGAG | p.Tyr559TrpfsTer4 | p.Y559Wfs*4 | P12956 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| XRCC6 | insertion | Nonsense_Mutation | novel | c.1786_1787insCTCCATCTCAAAAATGATACAG | p.Lys596ThrfsTer6 | p.K596Tfs*6 | P12956 | protein_coding | TCGA-BH-A0E2-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | ||
| XRCC6 | SNV | Missense_Mutation | novel | c.1366N>G | p.Pro456Ala | p.P456A | P12956 | protein_coding | tolerated(0.53) | benign(0.018) | TCGA-VS-A8EL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 |
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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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