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Gene: MSH6 |
Gene summary for MSH6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MSH6 | Gene ID | 2956 |
| Gene name | mutS homolog 6 | |
| Gene Alias | GTBP | |
| Cytomap | 2p16.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P52701 |
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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 |
| 2956 | MSH6 | LZE2T | Human | Esophagus | ESCC | 1.41e-02 | 9.04e-01 | 0.082 |
| 2956 | MSH6 | LZE4T | Human | Esophagus | ESCC | 1.01e-08 | 2.69e-01 | 0.0811 |
| 2956 | MSH6 | LZE7T | Human | Esophagus | ESCC | 1.87e-08 | 8.78e-01 | 0.0667 |
| 2956 | MSH6 | LZE8T | Human | Esophagus | ESCC | 8.87e-03 | 4.82e-02 | 0.067 |
| 2956 | MSH6 | LZE20T | Human | Esophagus | ESCC | 8.97e-03 | -5.55e-02 | 0.0662 |
| 2956 | MSH6 | LZE24T | Human | Esophagus | ESCC | 2.87e-06 | 2.40e-01 | 0.0596 |
| 2956 | MSH6 | LZE21T | Human | Esophagus | ESCC | 3.12e-02 | 1.14e-01 | 0.0655 |
| 2956 | MSH6 | P1T-E | Human | Esophagus | ESCC | 1.74e-02 | 3.47e-01 | 0.0875 |
| 2956 | MSH6 | P2T-E | Human | Esophagus | ESCC | 1.55e-56 | 1.29e+00 | 0.1177 |
| 2956 | MSH6 | P4T-E | Human | Esophagus | ESCC | 3.27e-15 | 5.00e-01 | 0.1323 |
| 2956 | MSH6 | P5T-E | Human | Esophagus | ESCC | 2.78e-08 | 3.67e-01 | 0.1327 |
| 2956 | MSH6 | P8T-E | Human | Esophagus | ESCC | 4.69e-13 | 2.62e-01 | 0.0889 |
| 2956 | MSH6 | P9T-E | Human | Esophagus | ESCC | 9.66e-03 | 1.39e-01 | 0.1131 |
| 2956 | MSH6 | P10T-E | Human | Esophagus | ESCC | 1.04e-18 | 4.93e-01 | 0.116 |
| 2956 | MSH6 | P11T-E | Human | Esophagus | ESCC | 3.54e-12 | 4.67e-01 | 0.1426 |
| 2956 | MSH6 | P12T-E | Human | Esophagus | ESCC | 7.42e-21 | 5.57e-01 | 0.1122 |
| 2956 | MSH6 | P15T-E | Human | Esophagus | ESCC | 7.87e-22 | 5.85e-01 | 0.1149 |
| 2956 | MSH6 | P16T-E | Human | Esophagus | ESCC | 1.75e-30 | 5.91e-01 | 0.1153 |
| 2956 | MSH6 | P17T-E | Human | Esophagus | ESCC | 2.54e-04 | 1.95e-01 | 0.1278 |
| 2956 | MSH6 | P20T-E | Human | Esophagus | ESCC | 5.15e-12 | 2.32e-01 | 0.1124 |
| Page: 1 2 3 4 5 |
| 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 | ||
| 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 | ||
| 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:0097193111 | Esophagus | ESCC | intrinsic apoptotic signaling pathway | 222/8552 | 288/18723 | 5.87e-28 | 2.02e-25 | 222 |
| GO:000941113 | Esophagus | ESCC | response to UV | 115/8552 | 149/18723 | 3.29e-15 | 1.93e-13 | 115 |
| GO:005105215 | Esophagus | ESCC | regulation of DNA metabolic process | 232/8552 | 359/18723 | 2.40e-13 | 1.13e-11 | 232 |
| GO:0008630110 | Esophagus | ESCC | intrinsic apoptotic signaling pathway in response to DNA damage | 78/8552 | 99/18723 | 1.43e-11 | 5.08e-10 | 78 |
| GO:000931419 | Esophagus | ESCC | response to radiation | 277/8552 | 456/18723 | 4.42e-11 | 1.43e-09 | 277 |
| GO:000756820 | Esophagus | ESCC | aging | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
| GO:000941611 | Esophagus | ESCC | response to light stimulus | 183/8552 | 320/18723 | 2.03e-05 | 1.76e-04 | 183 |
| 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: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:00164452 | Esophagus | ESCC | somatic diversification of immunoglobulins | 43/8552 | 67/18723 | 1.73e-03 | 7.97e-03 | 43 |
| GO:00023815 | Esophagus | ESCC | immunoglobulin production involved in immunoglobulin-mediated immune response | 44/8552 | 70/18723 | 2.80e-03 | 1.19e-02 | 44 |
| GO:00510951 | Esophagus | ESCC | regulation of helicase activity | 10/8552 | 12/18723 | 8.94e-03 | 3.12e-02 | 10 |
| GO:0002204 | Esophagus | ESCC | somatic recombination of immunoglobulin genes involved in immune response | 31/8552 | 49/18723 | 9.89e-03 | 3.40e-02 | 31 |
| GO:0002208 | Esophagus | ESCC | somatic diversification of immunoglobulins involved in immune response | 31/8552 | 49/18723 | 9.89e-03 | 3.40e-02 | 31 |
| GO:0045190 | Esophagus | ESCC | isotype switching | 31/8552 | 49/18723 | 9.89e-03 | 3.40e-02 | 31 |
| GO:009719322 | Liver | HCC | intrinsic apoptotic signaling pathway | 184/7958 | 288/18723 | 1.50e-13 | 8.32e-12 | 184 |
| GO:005105221 | Liver | HCC | regulation of DNA metabolic process | 198/7958 | 359/18723 | 7.62e-07 | 1.17e-05 | 198 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0521020 | Esophagus | ESCC | Colorectal cancer | 69/4205 | 86/8465 | 4.06e-09 | 4.13e-08 | 2.11e-08 | 69 |
| hsa015247 | Esophagus | ESCC | Platinum drug resistance | 56/4205 | 73/8465 | 1.85e-06 | 1.13e-05 | 5.78e-06 | 56 |
| hsa034304 | Esophagus | ESCC | Mismatch repair | 21/4205 | 23/8465 | 2.85e-05 | 1.35e-04 | 6.90e-05 | 21 |
| hsa05210110 | Esophagus | ESCC | Colorectal cancer | 69/4205 | 86/8465 | 4.06e-09 | 4.13e-08 | 2.11e-08 | 69 |
| hsa0152414 | Esophagus | ESCC | Platinum drug resistance | 56/4205 | 73/8465 | 1.85e-06 | 1.13e-05 | 5.78e-06 | 56 |
| hsa0343011 | Esophagus | ESCC | Mismatch repair | 21/4205 | 23/8465 | 2.85e-05 | 1.35e-04 | 6.90e-05 | 21 |
| hsa0521022 | Liver | HCC | Colorectal cancer | 65/4020 | 86/8465 | 8.85e-08 | 1.23e-06 | 6.87e-07 | 65 |
| hsa015242 | Liver | HCC | Platinum drug resistance | 52/4020 | 73/8465 | 3.14e-05 | 1.88e-04 | 1.04e-04 | 52 |
| hsa0521032 | Liver | HCC | Colorectal cancer | 65/4020 | 86/8465 | 8.85e-08 | 1.23e-06 | 6.87e-07 | 65 |
| hsa015243 | Liver | HCC | Platinum drug resistance | 52/4020 | 73/8465 | 3.14e-05 | 1.88e-04 | 1.04e-04 | 52 |
| hsa0521018 | Oral cavity | OSCC | Colorectal cancer | 66/3704 | 86/8465 | 3.99e-10 | 4.95e-09 | 2.52e-09 | 66 |
| hsa015246 | Oral cavity | OSCC | Platinum drug resistance | 51/3704 | 73/8465 | 5.41e-06 | 2.75e-05 | 1.40e-05 | 51 |
| hsa03430 | Oral cavity | OSCC | Mismatch repair | 19/3704 | 23/8465 | 1.55e-04 | 5.34e-04 | 2.72e-04 | 19 |
| hsa0521019 | Oral cavity | OSCC | Colorectal cancer | 66/3704 | 86/8465 | 3.99e-10 | 4.95e-09 | 2.52e-09 | 66 |
| hsa0152413 | Oral cavity | OSCC | Platinum drug resistance | 51/3704 | 73/8465 | 5.41e-06 | 2.75e-05 | 1.40e-05 | 51 |
| hsa034301 | Oral cavity | OSCC | Mismatch repair | 19/3704 | 23/8465 | 1.55e-04 | 5.34e-04 | 2.72e-04 | 19 |
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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 |
| MSH6 | SNV | Missense_Mutation | c.3146N>T | p.Ser1049Phe | p.S1049F | P52701 | protein_coding | deleterious(0.01) | benign(0.279) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| MSH6 | SNV | Missense_Mutation | c.3895N>T | p.Gly1299Cys | p.G1299C | P52701 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | |
| MSH6 | SNV | Missense_Mutation | c.1789N>C | p.Glu597Gln | p.E597Q | P52701 | protein_coding | deleterious(0) | probably_damaging(0.967) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| MSH6 | SNV | Missense_Mutation | rs773763465 | c.4000N>T | p.Arg1334Trp | p.R1334W | P52701 | protein_coding | deleterious(0) | probably_damaging(0.952) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| MSH6 | SNV | Missense_Mutation | c.2076A>C | p.Lys692Asn | p.K692N | P52701 | protein_coding | deleterious(0) | possibly_damaging(0.733) | TCGA-AO-A0J4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| MSH6 | SNV | Missense_Mutation | novel | c.2977N>A | p.Glu993Lys | p.E993K | P52701 | protein_coding | tolerated(0.14) | possibly_damaging(0.516) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MSH6 | SNV | Missense_Mutation | rs63750832 | c.2092N>G | p.Gln698Glu | p.Q698E | P52701 | protein_coding | tolerated(0.19) | benign(0.098) | TCGA-C8-A12Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| MSH6 | SNV | Missense_Mutation | c.2462N>C | p.Leu821Pro | p.L821P | P52701 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| MSH6 | SNV | Missense_Mutation | novel | c.1327N>A | p.Gly443Arg | p.G443R | P52701 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-OL-A5RU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | CR |
| MSH6 | insertion | Frame_Shift_Ins | rs748452299 | c.3253_3254insC | p.Phe1088LeufsTer5 | p.F1088Lfs*5 | P52701 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
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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 |
| 2956 | MSH6 | CLINICALLY ACTIONABLE, DNA REPAIR | Temozolomide | TEMOZOLOMIDE | 19584161 | |
| 2956 | MSH6 | CLINICALLY ACTIONABLE, DNA REPAIR | N/A | 21242281,19125127,26582061 | ||
| 2956 | MSH6 | CLINICALLY ACTIONABLE, DNA REPAIR | DURVALUMAB | DURVALUMAB | 26674132 | |
| 2956 | MSH6 | CLINICALLY ACTIONABLE, DNA REPAIR | KU60648 | 28224663 | ||
| 2956 | MSH6 | CLINICALLY ACTIONABLE, DNA REPAIR | ANTI-PD-1 MONOCLONAL ANTIBODY MEDI0680 | 26674132 | ||
| 2956 | MSH6 | CLINICALLY ACTIONABLE, DNA REPAIR | TEMOZOLOMIDE | TEMOZOLOMIDE | 17404084 |
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