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Gene: GLYR1 |
Gene summary for GLYR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GLYR1 | Gene ID | 84656 |
| Gene name | glyoxylate reductase 1 homolog | |
| Gene Alias | BM045 | |
| Cytomap | 16p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q49A26 |
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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 |
| 84656 | GLYR1 | LZE4T | Human | Esophagus | ESCC | 2.60e-07 | 2.85e-01 | 0.0811 |
| 84656 | GLYR1 | LZE7T | Human | Esophagus | ESCC | 2.20e-06 | 3.79e-01 | 0.0667 |
| 84656 | GLYR1 | LZE8T | Human | Esophagus | ESCC | 4.37e-04 | 1.63e-01 | 0.067 |
| 84656 | GLYR1 | LZE20T | Human | Esophagus | ESCC | 5.21e-03 | 1.59e-01 | 0.0662 |
| 84656 | GLYR1 | LZE21D1 | Human | Esophagus | HGIN | 3.55e-02 | 1.85e-01 | 0.0632 |
| 84656 | GLYR1 | LZE22D1 | Human | Esophagus | HGIN | 8.91e-05 | 1.07e-01 | 0.0595 |
| 84656 | GLYR1 | LZE22T | Human | Esophagus | ESCC | 2.86e-06 | 1.96e-01 | 0.068 |
| 84656 | GLYR1 | LZE24T | Human | Esophagus | ESCC | 3.90e-14 | 2.79e-01 | 0.0596 |
| 84656 | GLYR1 | LZE21T | Human | Esophagus | ESCC | 1.49e-05 | 1.41e-01 | 0.0655 |
| 84656 | GLYR1 | LZE6T | Human | Esophagus | ESCC | 1.61e-03 | 9.17e-02 | 0.0845 |
| 84656 | GLYR1 | P1T-E | Human | Esophagus | ESCC | 5.87e-12 | 6.11e-01 | 0.0875 |
| 84656 | GLYR1 | P2T-E | Human | Esophagus | ESCC | 3.22e-37 | 8.27e-01 | 0.1177 |
| 84656 | GLYR1 | P4T-E | Human | Esophagus | ESCC | 1.60e-19 | 2.63e-01 | 0.1323 |
| 84656 | GLYR1 | P5T-E | Human | Esophagus | ESCC | 1.11e-17 | 2.13e-01 | 0.1327 |
| 84656 | GLYR1 | P8T-E | Human | Esophagus | ESCC | 1.07e-24 | 4.14e-01 | 0.0889 |
| 84656 | GLYR1 | P9T-E | Human | Esophagus | ESCC | 6.98e-11 | 1.47e-01 | 0.1131 |
| 84656 | GLYR1 | P10T-E | Human | Esophagus | ESCC | 6.21e-18 | 2.44e-01 | 0.116 |
| 84656 | GLYR1 | P11T-E | Human | Esophagus | ESCC | 1.76e-10 | 4.50e-01 | 0.1426 |
| 84656 | GLYR1 | P12T-E | Human | Esophagus | ESCC | 2.55e-26 | 5.67e-01 | 0.1122 |
| 84656 | GLYR1 | P15T-E | Human | Esophagus | ESCC | 1.04e-26 | 5.82e-01 | 0.1149 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00182057 | Esophagus | HGIN | peptidyl-lysine modification | 88/2587 | 376/18723 | 2.99e-07 | 1.39e-05 | 88 |
| GO:00165708 | Esophagus | HGIN | histone modification | 92/2587 | 463/18723 | 1.70e-04 | 3.30e-03 | 92 |
| GO:00064735 | Esophagus | HGIN | protein acetylation | 45/2587 | 201/18723 | 6.17e-04 | 8.58e-03 | 45 |
| GO:00310568 | Esophagus | HGIN | regulation of histone modification | 36/2587 | 152/18723 | 7.06e-04 | 9.52e-03 | 36 |
| GO:00183945 | Esophagus | HGIN | peptidyl-lysine acetylation | 39/2587 | 169/18723 | 7.46e-04 | 9.90e-03 | 39 |
| GO:00435435 | Esophagus | HGIN | protein acylation | 51/2587 | 243/18723 | 1.33e-03 | 1.57e-02 | 51 |
| GO:00064755 | Esophagus | HGIN | internal protein amino acid acetylation | 36/2587 | 160/18723 | 1.87e-03 | 2.01e-02 | 36 |
| GO:00183935 | Esophagus | HGIN | internal peptidyl-lysine acetylation | 35/2587 | 158/18723 | 2.82e-03 | 2.75e-02 | 35 |
| GO:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
| GO:001820514 | Esophagus | ESCC | peptidyl-lysine modification | 259/8552 | 376/18723 | 3.90e-20 | 5.26e-18 | 259 |
| GO:001839413 | Esophagus | ESCC | peptidyl-lysine acetylation | 123/8552 | 169/18723 | 6.58e-13 | 2.94e-11 | 123 |
| GO:004354313 | Esophagus | ESCC | protein acylation | 165/8552 | 243/18723 | 1.69e-12 | 7.14e-11 | 165 |
| GO:000647313 | Esophagus | ESCC | protein acetylation | 140/8552 | 201/18723 | 4.37e-12 | 1.69e-10 | 140 |
| GO:001839313 | Esophagus | ESCC | internal peptidyl-lysine acetylation | 114/8552 | 158/18723 | 1.16e-11 | 4.24e-10 | 114 |
| GO:000647513 | Esophagus | ESCC | internal protein amino acid acetylation | 115/8552 | 160/18723 | 1.43e-11 | 5.08e-10 | 115 |
| GO:00165735 | Esophagus | ESCC | histone acetylation | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:003105614 | Esophagus | ESCC | regulation of histone modification | 106/8552 | 152/18723 | 1.52e-09 | 3.55e-08 | 106 |
| GO:00310583 | Esophagus | ESCC | positive regulation of histone modification | 65/8552 | 92/18723 | 1.04e-06 | 1.31e-05 | 65 |
| GO:20007564 | Esophagus | ESCC | regulation of peptidyl-lysine acetylation | 43/8552 | 63/18723 | 2.43e-04 | 1.50e-03 | 43 |
| GO:19019835 | Esophagus | ESCC | regulation of protein acetylation | 49/8552 | 77/18723 | 1.12e-03 | 5.60e-03 | 49 |
| Page: 1 2 3 4 5 6 7 |
| 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 |
| 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 |
| GLYR1 | SNV | Missense_Mutation | c.1559N>T | p.Pro520Leu | p.P520L | Q49A26 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GLYR1 | SNV | Missense_Mutation | c.622N>A | p.Glu208Lys | p.E208K | Q49A26 | protein_coding | tolerated(0.49) | benign(0.018) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| GLYR1 | SNV | Missense_Mutation | novel | c.1483N>C | p.Lys495Gln | p.K495Q | Q49A26 | protein_coding | tolerated(0.42) | benign(0.019) | TCGA-AN-A0XN-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| GLYR1 | SNV | Missense_Mutation | c.457N>A | p.Glu153Lys | p.E153K | Q49A26 | protein_coding | tolerated(0.53) | benign(0.012) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| GLYR1 | SNV | Missense_Mutation | c.1357G>A | p.Glu453Lys | p.E453K | Q49A26 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C8-A12T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| GLYR1 | insertion | Frame_Shift_Ins | novel | c.328_329insATATTGCCACTTGCCTTCCTGAAAGATTATGCCAGTTTACAGGGAGT | p.Arg110HisfsTer43 | p.R110Hfs*43 | Q49A26 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| GLYR1 | insertion | Frame_Shift_Ins | rs749150409 | c.1140dupG | p.Arg381AlafsTer15 | p.R381Afs*15 | Q49A26 | protein_coding | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| GLYR1 | SNV | Missense_Mutation | novel | c.452N>G | p.Ser151Cys | p.S151C | Q49A26 | protein_coding | deleterious(0.01) | probably_damaging(0.937) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| GLYR1 | SNV | Missense_Mutation | c.1494C>G | p.Phe498Leu | p.F498L | Q49A26 | protein_coding | tolerated(0.34) | benign(0.023) | TCGA-Q1-A6DW-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| GLYR1 | SNV | Missense_Mutation | novel | c.1585N>A | p.Glu529Lys | p.E529K | Q49A26 | protein_coding | deleterious(0) | benign(0.329) | TCGA-VS-A8QH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | gemcitabine | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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