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Gene: MSH2 |
Gene summary for MSH2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MSH2 | Gene ID | 4436 |
| Gene name | mutS homolog 2 | |
| Gene Alias | COCA1 | |
| Cytomap | 2p21-p16.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P43246 |
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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 |
| 4436 | MSH2 | LZE2T | Human | Esophagus | ESCC | 8.55e-03 | 4.87e-01 | 0.082 |
| 4436 | MSH2 | LZE4T | Human | Esophagus | ESCC | 2.91e-03 | 1.35e-01 | 0.0811 |
| 4436 | MSH2 | LZE7T | Human | Esophagus | ESCC | 6.11e-08 | 5.79e-01 | 0.0667 |
| 4436 | MSH2 | LZE24T | Human | Esophagus | ESCC | 1.02e-09 | 1.99e-01 | 0.0596 |
| 4436 | MSH2 | LZE6T | Human | Esophagus | ESCC | 7.15e-03 | 1.77e-01 | 0.0845 |
| 4436 | MSH2 | P1T-E | Human | Esophagus | ESCC | 1.42e-02 | 2.14e-01 | 0.0875 |
| 4436 | MSH2 | P2T-E | Human | Esophagus | ESCC | 2.77e-41 | 7.71e-01 | 0.1177 |
| 4436 | MSH2 | P4T-E | Human | Esophagus | ESCC | 2.47e-19 | 4.32e-01 | 0.1323 |
| 4436 | MSH2 | P5T-E | Human | Esophagus | ESCC | 7.84e-09 | 2.13e-01 | 0.1327 |
| 4436 | MSH2 | P8T-E | Human | Esophagus | ESCC | 9.46e-10 | 1.99e-01 | 0.0889 |
| 4436 | MSH2 | P9T-E | Human | Esophagus | ESCC | 1.74e-04 | 1.35e-01 | 0.1131 |
| 4436 | MSH2 | P10T-E | Human | Esophagus | ESCC | 3.16e-20 | 4.30e-01 | 0.116 |
| 4436 | MSH2 | P11T-E | Human | Esophagus | ESCC | 2.09e-04 | 2.39e-01 | 0.1426 |
| 4436 | MSH2 | P12T-E | Human | Esophagus | ESCC | 1.20e-17 | 3.69e-01 | 0.1122 |
| 4436 | MSH2 | P15T-E | Human | Esophagus | ESCC | 9.61e-14 | 3.49e-01 | 0.1149 |
| 4436 | MSH2 | P16T-E | Human | Esophagus | ESCC | 1.04e-24 | 5.07e-01 | 0.1153 |
| 4436 | MSH2 | P17T-E | Human | Esophagus | ESCC | 2.49e-02 | 1.14e-01 | 0.1278 |
| 4436 | MSH2 | P19T-E | Human | Esophagus | ESCC | 3.82e-02 | 3.48e-01 | 0.1662 |
| 4436 | MSH2 | P20T-E | Human | Esophagus | ESCC | 4.08e-11 | 1.87e-01 | 0.1124 |
| 4436 | MSH2 | P21T-E | Human | Esophagus | ESCC | 2.60e-14 | 3.33e-01 | 0.1617 |
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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 | ||
| 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 |
| ∗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:19031316 | Oral cavity | OSCC | mononuclear cell differentiation | 210/7305 | 426/18723 | 8.44e-06 | 9.02e-05 | 210 |
| GO:00315704 | Oral cavity | OSCC | DNA integrity checkpoint | 72/7305 | 123/18723 | 8.77e-06 | 9.31e-05 | 72 |
| GO:00000774 | Oral cavity | OSCC | DNA damage checkpoint | 67/7305 | 115/18723 | 2.20e-05 | 2.08e-04 | 67 |
| GO:00447744 | Oral cavity | OSCC | mitotic DNA integrity checkpoint | 52/7305 | 85/18723 | 2.86e-05 | 2.64e-04 | 52 |
| GO:00447734 | Oral cavity | OSCC | mitotic DNA damage checkpoint | 50/7305 | 81/18723 | 2.87e-05 | 2.64e-04 | 50 |
| GO:004352310 | Oral cavity | OSCC | regulation of neuron apoptotic process | 111/7305 | 212/18723 | 5.12e-05 | 4.27e-04 | 111 |
| GO:00094164 | Oral cavity | OSCC | response to light stimulus | 159/7305 | 320/18723 | 5.98e-05 | 4.92e-04 | 159 |
| GO:00300983 | Oral cavity | OSCC | lymphocyte differentiation | 179/7305 | 374/18723 | 2.74e-04 | 1.74e-03 | 179 |
| GO:0006310 | Oral cavity | OSCC | DNA recombination | 147/7305 | 305/18723 | 6.33e-04 | 3.56e-03 | 147 |
| GO:19012159 | Oral cavity | OSCC | negative regulation of neuron death | 104/7305 | 208/18723 | 7.90e-04 | 4.27e-03 | 104 |
| GO:00101652 | Oral cavity | OSCC | response to X-ray | 22/7305 | 33/18723 | 1.19e-03 | 6.03e-03 | 22 |
| GO:0051095 | Oral cavity | OSCC | regulation of helicase activity | 10/7305 | 12/18723 | 2.25e-03 | 1.00e-02 | 10 |
| GO:00063011 | Oral cavity | OSCC | postreplication repair | 20/7305 | 31/18723 | 3.57e-03 | 1.49e-02 | 20 |
| GO:00027022 | Oral cavity | OSCC | positive regulation of production of molecular mediator of immune response | 58/7305 | 117/18723 | 1.28e-02 | 4.27e-02 | 58 |
| GO:00023814 | Oral cavity | OSCC | immunoglobulin production involved in immunoglobulin-mediated immune response | 37/7305 | 70/18723 | 1.28e-02 | 4.28e-02 | 37 |
| GO:0016447 | Oral cavity | OSCC | somatic recombination of immunoglobulin gene segments | 31/7305 | 57/18723 | 1.32e-02 | 4.38e-02 | 31 |
| GO:00022002 | Oral cavity | OSCC | somatic diversification of immune receptors | 40/7305 | 77/18723 | 1.42e-02 | 4.69e-02 | 40 |
| GO:0002562 | Oral cavity | OSCC | somatic diversification of immune receptors via germline recombination within a single locus | 35/7305 | 66/18723 | 1.43e-02 | 4.69e-02 | 35 |
| GO:0016444 | Oral cavity | OSCC | somatic cell DNA recombination | 35/7305 | 66/18723 | 1.43e-02 | 4.69e-02 | 35 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 |
| hsa052107 | Liver | Cirrhotic | Colorectal cancer | 39/2530 | 86/8465 | 1.67e-03 | 8.01e-03 | 4.94e-03 | 39 |
| hsa0521012 | Liver | Cirrhotic | Colorectal cancer | 39/2530 | 86/8465 | 1.67e-03 | 8.01e-03 | 4.94e-03 | 39 |
| 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 |
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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. |
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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 |
| MSH2 | SNV | Missense_Mutation | novel | c.1315N>A | p.Pro439Thr | p.P439T | P43246 | protein_coding | deleterious(0.01) | probably_damaging(0.994) | TCGA-A7-A3RF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD |
| MSH2 | SNV | Missense_Mutation | c.1351N>G | p.Gln451Glu | p.Q451E | P43246 | protein_coding | tolerated(0.17) | benign(0.14) | TCGA-A8-A09Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD | |
| MSH2 | SNV | Missense_Mutation | c.2573N>C | p.Gly858Ala | p.G858A | P43246 | protein_coding | tolerated(0.19) | benign(0.007) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| MSH2 | SNV | Missense_Mutation | c.1976N>C | p.Lys659Thr | p.K659T | P43246 | protein_coding | deleterious(0) | possibly_damaging(0.833) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| MSH2 | SNV | Missense_Mutation | c.1228N>A | p.Gly410Ser | p.G410S | P43246 | protein_coding | tolerated(0.17) | benign(0.006) | TCGA-BH-A0BZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |
| MSH2 | SNV | Missense_Mutation | rs587782355 | c.1530N>C | p.Gln510His | p.Q510H | P43246 | protein_coding | deleterious(0.03) | benign(0.014) | TCGA-D8-A1J9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MSH2 | SNV | Missense_Mutation | rs772662439 | c.2197N>A | p.Ala733Thr | p.A733T | P43246 | protein_coding | deleterious(0) | probably_damaging(0.954) | TCGA-DG-A2KL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| MSH2 | SNV | Missense_Mutation | c.643C>G | p.Gln215Glu | p.Q215E | P43246 | protein_coding | tolerated(0.34) | benign(0.04) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD | |
| MSH2 | SNV | Missense_Mutation | rs372189599 | c.174C>G | p.Phe58Leu | p.F58L | P43246 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-EK-A2R7-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| MSH2 | insertion | Frame_Shift_Ins | novel | c.2425_2426insCACAT | p.Glu809AlafsTer5 | p.E809Afs*5 | P43246 | protein_coding | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | 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 |
| 4436 | MSH2 | CLINICALLY ACTIONABLE, DNA REPAIR | ANTI-PD-1 MONOCLONAL ANTIBODY MEDI0680 | 26674132 | ||
| 4436 | MSH2 | CLINICALLY ACTIONABLE, DNA REPAIR | DURVALUMAB | DURVALUMAB | 26674132 |
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