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Gene: MR1 |
Gene summary for MR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MR1 | Gene ID | 3140 |
| Gene name | major histocompatibility complex, class I-related | |
| Gene Alias | HLALS | |
| Cytomap | 1q25.3 | |
| Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | Q95460 |
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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 |
| 3140 | MR1 | LZE4T | Human | Esophagus | ESCC | 4.23e-09 | 1.75e-01 | 0.0811 |
| 3140 | MR1 | LZE20T | Human | Esophagus | ESCC | 1.24e-02 | 9.35e-02 | 0.0662 |
| 3140 | MR1 | LZE24T | Human | Esophagus | ESCC | 1.39e-07 | 2.86e-01 | 0.0596 |
| 3140 | MR1 | P2T-E | Human | Esophagus | ESCC | 2.79e-16 | 3.69e-01 | 0.1177 |
| 3140 | MR1 | P4T-E | Human | Esophagus | ESCC | 3.81e-14 | 3.26e-01 | 0.1323 |
| 3140 | MR1 | P5T-E | Human | Esophagus | ESCC | 1.52e-03 | 1.32e-01 | 0.1327 |
| 3140 | MR1 | P8T-E | Human | Esophagus | ESCC | 7.17e-17 | 2.34e-01 | 0.0889 |
| 3140 | MR1 | P9T-E | Human | Esophagus | ESCC | 4.71e-02 | 6.38e-02 | 0.1131 |
| 3140 | MR1 | P10T-E | Human | Esophagus | ESCC | 2.28e-08 | 1.71e-01 | 0.116 |
| 3140 | MR1 | P11T-E | Human | Esophagus | ESCC | 1.45e-05 | 2.00e-01 | 0.1426 |
| 3140 | MR1 | P12T-E | Human | Esophagus | ESCC | 1.15e-10 | 1.61e-01 | 0.1122 |
| 3140 | MR1 | P15T-E | Human | Esophagus | ESCC | 1.48e-09 | 2.04e-01 | 0.1149 |
| 3140 | MR1 | P16T-E | Human | Esophagus | ESCC | 4.90e-06 | 1.38e-01 | 0.1153 |
| 3140 | MR1 | P20T-E | Human | Esophagus | ESCC | 4.36e-14 | 2.76e-01 | 0.1124 |
| 3140 | MR1 | P21T-E | Human | Esophagus | ESCC | 3.11e-17 | 2.21e-01 | 0.1617 |
| 3140 | MR1 | P22T-E | Human | Esophagus | ESCC | 1.78e-11 | 1.69e-01 | 0.1236 |
| 3140 | MR1 | P23T-E | Human | Esophagus | ESCC | 1.55e-09 | 3.38e-01 | 0.108 |
| 3140 | MR1 | P24T-E | Human | Esophagus | ESCC | 1.81e-11 | 1.74e-01 | 0.1287 |
| 3140 | MR1 | P26T-E | Human | Esophagus | ESCC | 1.21e-05 | 7.27e-02 | 0.1276 |
| 3140 | MR1 | P27T-E | Human | Esophagus | ESCC | 2.83e-10 | 1.71e-01 | 0.1055 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:006099623 | Thyroid | ATC | dendritic spine development | 57/6293 | 99/18723 | 8.24e-07 | 1.09e-05 | 57 |
| GO:0060491111 | Thyroid | ATC | regulation of cell projection assembly | 95/6293 | 188/18723 | 1.14e-06 | 1.47e-05 | 95 |
| GO:000689826 | Thyroid | ATC | receptor-mediated endocytosis | 118/6293 | 244/18723 | 1.17e-06 | 1.50e-05 | 118 |
| GO:200102214 | Thyroid | ATC | positive regulation of response to DNA damage stimulus | 59/6293 | 105/18723 | 1.62e-06 | 1.97e-05 | 59 |
| GO:1903312210 | Thyroid | ATC | negative regulation of mRNA metabolic process | 53/6293 | 92/18723 | 1.93e-06 | 2.32e-05 | 53 |
| GO:190390028 | Thyroid | ATC | regulation of viral life cycle | 77/6293 | 148/18723 | 2.79e-06 | 3.21e-05 | 77 |
| GO:003105811 | Thyroid | ATC | positive regulation of histone modification | 52/6293 | 92/18723 | 5.21e-06 | 5.61e-05 | 52 |
| GO:005185121 | Thyroid | ATC | modulation by host of symbiont process | 37/6293 | 60/18723 | 7.87e-06 | 8.04e-05 | 37 |
| GO:001988229 | Thyroid | ATC | antigen processing and presentation | 57/6293 | 106/18723 | 1.48e-05 | 1.39e-04 | 57 |
| GO:004311224 | Thyroid | ATC | receptor metabolic process | 82/6293 | 166/18723 | 1.78e-05 | 1.63e-04 | 82 |
| GO:006014823 | Thyroid | ATC | positive regulation of posttranscriptional gene silencing | 22/6293 | 31/18723 | 2.35e-05 | 2.06e-04 | 22 |
| GO:000038126 | Thyroid | ATC | regulation of alternative mRNA splicing, via spliceosome | 36/6293 | 60/18723 | 2.48e-05 | 2.16e-04 | 36 |
| GO:001631117 | Thyroid | ATC | dephosphorylation | 179/6293 | 417/18723 | 3.88e-05 | 3.15e-04 | 179 |
| GO:006099815 | Thyroid | ATC | regulation of dendritic spine development | 36/6293 | 61/18723 | 4.10e-05 | 3.32e-04 | 36 |
| GO:000283123 | Thyroid | ATC | regulation of response to biotic stimulus | 144/6293 | 327/18723 | 4.94e-05 | 3.91e-04 | 144 |
| GO:00514911 | Thyroid | ATC | positive regulation of filopodium assembly | 21/6293 | 30/18723 | 5.03e-05 | 3.96e-04 | 21 |
| GO:200063724 | Thyroid | ATC | positive regulation of gene silencing by miRNA | 21/6293 | 30/18723 | 5.03e-05 | 3.96e-04 | 21 |
| GO:004825931 | Thyroid | ATC | regulation of receptor-mediated endocytosis | 57/6293 | 110/18723 | 6.05e-05 | 4.63e-04 | 57 |
| GO:00514892 | Thyroid | ATC | regulation of filopodium assembly | 29/6293 | 47/18723 | 7.37e-05 | 5.60e-04 | 29 |
| GO:003582121 | Thyroid | ATC | modulation of process of other organism | 55/6293 | 106/18723 | 7.71e-05 | 5.82e-04 | 55 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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. |
| 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 |
| MR1 | SNV | Missense_Mutation | c.1022G>A | p.Arg341Gln | p.R341Q | Q95460 | protein_coding | tolerated_low_confidence(1) | benign(0) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| MR1 | SNV | Missense_Mutation | c.334C>G | p.His112Asp | p.H112D | Q95460 | protein_coding | deleterious(0) | benign(0.393) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| MR1 | SNV | Missense_Mutation | c.176A>G | p.Asp59Gly | p.D59G | Q95460 | protein_coding | deleterious(0) | benign(0.371) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| MR1 | SNV | Missense_Mutation | c.65N>T | p.Ser22Phe | p.S22F | Q95460 | protein_coding | deleterious(0.01) | benign(0.06) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| MR1 | SNV | Missense_Mutation | novel | c.382A>G | p.Thr128Ala | p.T128A | Q95460 | protein_coding | tolerated(0.08) | possibly_damaging(0.682) | TCGA-OL-A6VR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MR1 | SNV | Missense_Mutation | novel | c.148G>A | p.Val50Met | p.V50M | Q95460 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| MR1 | SNV | Missense_Mutation | novel | c.823N>G | p.Leu275Val | p.L275V | Q95460 | protein_coding | tolerated(0.62) | benign(0.005) | TCGA-VS-A8EK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| MR1 | SNV | Missense_Mutation | rs377066166 | c.816N>A | p.Ser272Arg | p.S272R | Q95460 | protein_coding | deleterious(0.04) | possibly_damaging(0.452) | TCGA-A6-6782-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| MR1 | SNV | Missense_Mutation | rs775161220 | c.137C>T | p.Ser46Leu | p.S46L | Q95460 | protein_coding | tolerated(0.1) | probably_damaging(0.998) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| MR1 | SNV | Missense_Mutation | rs775161220 | c.137C>T | p.Ser46Leu | p.S46L | Q95460 | protein_coding | tolerated(0.1) | probably_damaging(0.998) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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 |
| 3140 | MR1 | DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE | ANTITHYMOCYTE GLOBULIN |
| Page: 1 |
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