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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:00350653 | Esophagus | ESCC | regulation of histone acetylation | 36/8552 | 54/18723 | 1.49e-03 | 7.06e-03 | 36 |
| GO:00165703 | Liver | NAFLD | histone modification | 90/1882 | 463/18723 | 5.74e-10 | 1.28e-07 | 90 |
| GO:0018205 | Liver | NAFLD | peptidyl-lysine modification | 65/1882 | 376/18723 | 9.42e-06 | 3.02e-04 | 65 |
| GO:0043543 | Liver | NAFLD | protein acylation | 43/1882 | 243/18723 | 1.70e-04 | 3.07e-03 | 43 |
| GO:0006473 | Liver | NAFLD | protein acetylation | 37/1882 | 201/18723 | 2.10e-04 | 3.61e-03 | 37 |
| GO:0018394 | Liver | NAFLD | peptidyl-lysine acetylation | 32/1882 | 169/18723 | 3.24e-04 | 5.00e-03 | 32 |
| GO:00310563 | Liver | NAFLD | regulation of histone modification | 29/1882 | 152/18723 | 5.30e-04 | 7.31e-03 | 29 |
| GO:0018393 | Liver | NAFLD | internal peptidyl-lysine acetylation | 28/1882 | 158/18723 | 2.10e-03 | 2.06e-02 | 28 |
| GO:0006475 | Liver | NAFLD | internal protein amino acid acetylation | 28/1882 | 160/18723 | 2.54e-03 | 2.36e-02 | 28 |
| GO:0016573 | Liver | NAFLD | histone acetylation | 26/1882 | 152/18723 | 4.85e-03 | 3.84e-02 | 26 |
| GO:00064731 | Liver | Cirrhotic | protein acetylation | 84/4634 | 201/18723 | 7.50e-08 | 2.25e-06 | 84 |
| GO:00183941 | Liver | Cirrhotic | peptidyl-lysine acetylation | 73/4634 | 169/18723 | 1.08e-07 | 3.07e-06 | 73 |
| GO:00435431 | Liver | Cirrhotic | protein acylation | 95/4634 | 243/18723 | 4.73e-07 | 1.07e-05 | 95 |
| GO:00182051 | Liver | Cirrhotic | peptidyl-lysine modification | 134/4634 | 376/18723 | 1.29e-06 | 2.59e-05 | 134 |
| GO:00064751 | Liver | Cirrhotic | internal protein amino acid acetylation | 65/4634 | 160/18723 | 6.66e-06 | 1.04e-04 | 65 |
| GO:00183931 | Liver | Cirrhotic | internal peptidyl-lysine acetylation | 64/4634 | 158/18723 | 8.75e-06 | 1.29e-04 | 64 |
| GO:001657011 | Liver | Cirrhotic | histone modification | 154/4634 | 463/18723 | 1.92e-05 | 2.57e-04 | 154 |
| GO:00165731 | Liver | Cirrhotic | histone acetylation | 61/4634 | 152/18723 | 1.97e-05 | 2.62e-04 | 61 |
| GO:2000756 | Liver | Cirrhotic | regulation of peptidyl-lysine acetylation | 30/4634 | 63/18723 | 6.83e-05 | 7.74e-04 | 30 |
| GO:003105611 | Liver | Cirrhotic | regulation of histone modification | 59/4634 | 152/18723 | 8.28e-05 | 9.02e-04 | 59 |
| 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 |
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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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