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Gene: MSRA |
Gene summary for MSRA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MSRA | Gene ID | 4482 |
| Gene name | methionine sulfoxide reductase A | |
| Gene Alias | PMSR | |
| Cytomap | 8p23.1 | |
| Gene Type | protein-coding | GO ID | GO:0000096 | UniProtAcc | Q9UJ68 |
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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 |
| 4482 | MSRA | P1T-E | Human | Esophagus | ESCC | 1.44e-03 | 2.29e-01 | 0.0875 |
| 4482 | MSRA | P2T-E | Human | Esophagus | ESCC | 7.70e-23 | 5.07e-01 | 0.1177 |
| 4482 | MSRA | P5T-E | Human | Esophagus | ESCC | 6.29e-05 | 9.29e-03 | 0.1327 |
| 4482 | MSRA | P8T-E | Human | Esophagus | ESCC | 1.68e-12 | 1.27e-01 | 0.0889 |
| 4482 | MSRA | P10T-E | Human | Esophagus | ESCC | 2.44e-08 | 1.60e-01 | 0.116 |
| 4482 | MSRA | P12T-E | Human | Esophagus | ESCC | 4.32e-03 | -3.96e-02 | 0.1122 |
| 4482 | MSRA | P16T-E | Human | Esophagus | ESCC | 1.46e-22 | 4.04e-01 | 0.1153 |
| 4482 | MSRA | P17T-E | Human | Esophagus | ESCC | 7.34e-07 | 2.30e-01 | 0.1278 |
| 4482 | MSRA | P21T-E | Human | Esophagus | ESCC | 1.32e-04 | 1.92e-01 | 0.1617 |
| 4482 | MSRA | P22T-E | Human | Esophagus | ESCC | 1.35e-17 | 2.14e-01 | 0.1236 |
| 4482 | MSRA | P24T-E | Human | Esophagus | ESCC | 2.62e-15 | 2.94e-01 | 0.1287 |
| 4482 | MSRA | P26T-E | Human | Esophagus | ESCC | 1.90e-04 | 5.42e-02 | 0.1276 |
| 4482 | MSRA | P27T-E | Human | Esophagus | ESCC | 9.04e-08 | -3.21e-03 | 0.1055 |
| 4482 | MSRA | P28T-E | Human | Esophagus | ESCC | 1.33e-06 | 6.73e-02 | 0.1149 |
| 4482 | MSRA | P30T-E | Human | Esophagus | ESCC | 1.83e-14 | 5.46e-01 | 0.137 |
| 4482 | MSRA | P32T-E | Human | Esophagus | ESCC | 1.95e-19 | 3.74e-01 | 0.1666 |
| 4482 | MSRA | P36T-E | Human | Esophagus | ESCC | 2.74e-08 | 2.71e-01 | 0.1187 |
| 4482 | MSRA | P37T-E | Human | Esophagus | ESCC | 7.63e-03 | -7.75e-03 | 0.1371 |
| 4482 | MSRA | P47T-E | Human | Esophagus | ESCC | 1.42e-09 | 1.29e-01 | 0.1067 |
| 4482 | MSRA | P48T-E | Human | Esophagus | ESCC | 1.45e-15 | 9.13e-02 | 0.0959 |
| Page: 1 2 3 |
| 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 | ||
| 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:0006979111 | Esophagus | ESCC | response to oxidative stress | 303/8552 | 446/18723 | 7.15e-22 | 1.30e-19 | 303 |
| GO:0062197111 | Esophagus | ESCC | cellular response to chemical stress | 234/8552 | 337/18723 | 5.37e-19 | 5.97e-17 | 234 |
| GO:0034599111 | Esophagus | ESCC | cellular response to oxidative stress | 197/8552 | 288/18723 | 3.76e-15 | 2.15e-13 | 197 |
| GO:00067906 | Esophagus | ESCC | sulfur compound metabolic process | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
| GO:000697920 | Oral cavity | OSCC | response to oxidative stress | 273/7305 | 446/18723 | 8.35e-22 | 1.65e-19 | 273 |
| GO:006219720 | Oral cavity | OSCC | cellular response to chemical stress | 204/7305 | 337/18723 | 6.89e-16 | 5.19e-14 | 204 |
| GO:003459920 | Oral cavity | OSCC | cellular response to oxidative stress | 173/7305 | 288/18723 | 2.90e-13 | 1.43e-11 | 173 |
| GO:00067905 | Oral cavity | OSCC | sulfur compound metabolic process | 168/7305 | 339/18723 | 4.50e-05 | 3.84e-04 | 168 |
| GO:000697926 | Oral cavity | EOLP | response to oxidative stress | 87/2218 | 446/18723 | 1.62e-06 | 3.80e-05 | 87 |
| GO:006219726 | Oral cavity | EOLP | cellular response to chemical stress | 64/2218 | 337/18723 | 8.49e-05 | 1.01e-03 | 64 |
| GO:003459925 | Oral cavity | EOLP | cellular response to oxidative stress | 54/2218 | 288/18723 | 4.04e-04 | 3.58e-03 | 54 |
| GO:000697933 | Oral cavity | NEOLP | response to oxidative stress | 94/2005 | 446/18723 | 7.53e-11 | 8.58e-09 | 94 |
| GO:006219733 | Oral cavity | NEOLP | cellular response to chemical stress | 75/2005 | 337/18723 | 4.87e-10 | 3.97e-08 | 75 |
| GO:003459933 | Oral cavity | NEOLP | cellular response to oxidative stress | 61/2005 | 288/18723 | 1.33e-07 | 4.67e-06 | 61 |
| GO:0006979113 | Thyroid | PTC | response to oxidative stress | 234/5968 | 446/18723 | 6.97e-20 | 9.77e-18 | 234 |
| GO:0062197113 | Thyroid | PTC | cellular response to chemical stress | 180/5968 | 337/18723 | 1.36e-16 | 1.16e-14 | 180 |
| GO:0034599113 | Thyroid | PTC | cellular response to oxidative stress | 151/5968 | 288/18723 | 2.82e-13 | 1.43e-11 | 151 |
| GO:00065552 | Thyroid | PTC | methionine metabolic process | 11/5968 | 16/18723 | 2.70e-03 | 1.36e-02 | 11 |
| GO:00000963 | Thyroid | PTC | sulfur amino acid metabolic process | 18/5968 | 34/18723 | 8.65e-03 | 3.62e-02 | 18 |
| GO:000697934 | Thyroid | ATC | response to oxidative stress | 246/6293 | 446/18723 | 2.98e-21 | 6.09e-19 | 246 |
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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 |
| MSRA | SNV | Missense_Mutation | novel | c.298N>G | p.Thr100Ala | p.T100A | Q9UJ68 | protein_coding | deleterious(0) | probably_damaging(0.923) | TCGA-A2-A0EP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | CR |
| MSRA | SNV | Missense_Mutation | novel | c.274C>G | p.Gln92Glu | p.Q92E | Q9UJ68 | protein_coding | deleterious(0.01) | possibly_damaging(0.85) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
| MSRA | SNV | Missense_Mutation | c.131N>T | p.Thr44Ile | p.T44I | Q9UJ68 | protein_coding | tolerated(0.92) | benign(0) | TCGA-AZ-6599-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| MSRA | SNV | Missense_Mutation | c.443N>A | p.Arg148His | p.R148H | Q9UJ68 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-CM-6166-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| MSRA | SNV | Missense_Mutation | rs755860421 | c.622N>A | p.His208Asn | p.H208N | Q9UJ68 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MSRA | SNV | Missense_Mutation | novel | c.376G>A | p.Glu126Lys | p.E126K | Q9UJ68 | protein_coding | tolerated(0.67) | benign(0.031) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| MSRA | SNV | Missense_Mutation | novel | c.26G>A | p.Cys9Tyr | p.C9Y | Q9UJ68 | protein_coding | tolerated_low_confidence(0.28) | benign(0.006) | TCGA-AJ-A2QO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MSRA | SNV | Missense_Mutation | novel | c.436N>T | p.Gly146Cys | p.G146C | Q9UJ68 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| MSRA | SNV | Missense_Mutation | novel | c.239N>T | p.Arg80Met | p.R80M | Q9UJ68 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| MSRA | SNV | Missense_Mutation | rs780558371 | c.454N>A | p.Asp152Asn | p.D152N | Q9UJ68 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | 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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