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Gene: XRCC2 |
Gene summary for XRCC2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | XRCC2 | Gene ID | 7516 |
| Gene name | X-ray repair cross complementing 2 | |
| Gene Alias | FANCU | |
| Cytomap | 7q36.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | O43543 |
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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 |
| 7516 | XRCC2 | HCC1_Meng | Human | Liver | HCC | 1.43e-11 | 2.88e-02 | 0.0246 |
| 7516 | XRCC2 | HCC2 | Human | Liver | HCC | 4.65e-08 | 2.19e+00 | 0.5341 |
| 7516 | XRCC2 | HCC5 | Human | Liver | HCC | 3.20e-04 | 5.72e-01 | 0.4932 |
| 7516 | XRCC2 | ATC13 | Human | Thyroid | ATC | 4.82e-02 | 9.53e-02 | 0.34 |
| 7516 | XRCC2 | ATC2 | Human | Thyroid | ATC | 5.35e-04 | 5.03e-01 | 0.34 |
| 7516 | XRCC2 | ATC4 | Human | Thyroid | ATC | 2.74e-03 | 1.22e-01 | 0.34 |
| 7516 | XRCC2 | ATC5 | Human | Thyroid | ATC | 5.43e-04 | 1.46e-01 | 0.34 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:007099722 | Liver | HCC | neuron death | 202/7958 | 361/18723 | 1.44e-07 | 2.70e-06 | 202 |
| GO:000170111 | Liver | HCC | in utero embryonic development | 204/7958 | 367/18723 | 2.44e-07 | 4.30e-06 | 204 |
| GO:190121412 | Liver | HCC | regulation of neuron death | 179/7958 | 319/18723 | 5.65e-07 | 9.01e-06 | 179 |
| GO:001021221 | Liver | HCC | response to ionizing radiation | 89/7958 | 148/18723 | 1.10e-05 | 1.26e-04 | 89 |
| GO:005140212 | Liver | HCC | neuron apoptotic process | 135/7958 | 246/18723 | 5.64e-05 | 5.26e-04 | 135 |
| GO:004352312 | Liver | HCC | regulation of neuron apoptotic process | 117/7958 | 212/18723 | 1.25e-04 | 1.03e-03 | 117 |
| GO:0031023 | Liver | HCC | microtubule organizing center organization | 82/7958 | 143/18723 | 2.38e-04 | 1.79e-03 | 82 |
| GO:00103321 | Liver | HCC | response to gamma radiation | 37/7958 | 56/18723 | 3.13e-04 | 2.22e-03 | 37 |
| GO:0007098 | Liver | HCC | centrosome cycle | 75/7958 | 130/18723 | 3.33e-04 | 2.34e-03 | 75 |
| GO:190121512 | Liver | HCC | negative regulation of neuron death | 113/7958 | 208/18723 | 3.68e-04 | 2.54e-03 | 113 |
| GO:001072011 | Liver | HCC | positive regulation of cell development | 155/7958 | 298/18723 | 5.39e-04 | 3.48e-03 | 155 |
| GO:00063021 | Liver | HCC | double-strand break repair | 131/7958 | 251/18723 | 1.17e-03 | 6.54e-03 | 131 |
| GO:00507674 | Liver | HCC | regulation of neurogenesis | 181/7958 | 364/18723 | 3.00e-03 | 1.40e-02 | 181 |
| GO:00093146 | Liver | HCC | response to radiation | 223/7958 | 456/18723 | 3.08e-03 | 1.43e-02 | 223 |
| GO:00507693 | Liver | HCC | positive regulation of neurogenesis | 116/7958 | 225/18723 | 3.67e-03 | 1.63e-02 | 116 |
| GO:003526421 | Liver | HCC | multicellular organism growth | 70/7958 | 132/18723 | 9.29e-03 | 3.57e-02 | 70 |
| GO:000170126 | Thyroid | ATC | in utero embryonic development | 183/6293 | 367/18723 | 6.62e-11 | 2.11e-09 | 183 |
| GO:0070997210 | Thyroid | ATC | neuron death | 176/6293 | 361/18723 | 1.43e-09 | 3.57e-08 | 176 |
| GO:190121428 | Thyroid | ATC | regulation of neuron death | 156/6293 | 319/18723 | 9.30e-09 | 1.96e-07 | 156 |
| GO:000931426 | Thyroid | ATC | response to radiation | 210/6293 | 456/18723 | 1.69e-08 | 3.39e-07 | 210 |
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| 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 |
| XRCC2 | SNV | Missense_Mutation | rs775565256 | c.581N>T | p.Thr194Met | p.T194M | O43543 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-A1-A0SQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | ac | SD |
| XRCC2 | SNV | Missense_Mutation | c.307N>C | p.Ser103Arg | p.S103R | O43543 | protein_coding | tolerated(0.15) | possibly_damaging(0.449) | TCGA-A2-A0D0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| XRCC2 | SNV | Missense_Mutation | c.541G>A | p.Glu181Lys | p.E181K | O43543 | protein_coding | tolerated(0.4) | benign(0.005) | TCGA-E2-A1LH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| XRCC2 | insertion | Frame_Shift_Ins | novel | c.12_13insAGGAATTTTCTAATGACGTATTTTG | p.Phe5ArgfsTer11 | p.F5Rfs*11 | O43543 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| XRCC2 | insertion | Nonsense_Mutation | novel | c.377_378insTCTCCAATAATAAAAAAATGTTTTTTTAAACTGTT | p.Leu126PhefsTer4 | p.L126Ffs*4 | O43543 | protein_coding | TCGA-B6-A0RI-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| XRCC2 | SNV | Missense_Mutation | rs775565256 | c.581C>T | p.Thr194Met | p.T194M | O43543 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| XRCC2 | SNV | Missense_Mutation | rs730882047 | c.770N>T | p.Ser257Leu | p.S257L | O43543 | protein_coding | tolerated(0.31) | benign(0.084) | TCGA-VS-A8EL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| XRCC2 | SNV | Missense_Mutation | c.421N>T | p.Pro141Ser | p.P141S | O43543 | protein_coding | deleterious(0) | possibly_damaging(0.874) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| XRCC2 | SNV | Missense_Mutation | c.659A>G | p.Asp220Gly | p.D220G | O43543 | protein_coding | tolerated(0.14) | benign(0.001) | TCGA-AA-3821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| XRCC2 | SNV | Missense_Mutation | c.213N>C | p.Glu71Asp | p.E71D | O43543 | protein_coding | tolerated(0.59) | benign(0.007) | TCGA-AA-3966-01 | 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 |
| Page: 1 |
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