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Gene: GLRA2 |
Gene summary for GLRA2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GLRA2 | Gene ID | 2742 |
| Gene name | glycine receptor alpha 2 | |
| Gene Alias | GLR | |
| Cytomap | Xp22.2 | |
| Gene Type | protein-coding | GO ID | GO:0001101 | UniProtAcc | P23416 |
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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 |
| 2742 | GLRA2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.82e-04 | 2.15e-01 | 0.281 |
| 2742 | GLRA2 | A002-C-010 | Human | Colorectum | FAP | 8.38e-08 | 3.82e-01 | 0.242 |
| 2742 | GLRA2 | A002-C-021 | Human | Colorectum | FAP | 5.31e-16 | 5.06e-01 | 0.1171 |
| 2742 | GLRA2 | A002-C-016 | Human | Colorectum | FAP | 1.85e-03 | 2.87e-01 | 0.0521 |
| 2742 | GLRA2 | A014-C-008 | Human | Colorectum | FAP | 1.77e-04 | 4.37e-01 | -0.191 |
| 2742 | GLRA2 | F072B | Human | Colorectum | FAP | 5.57e-10 | 4.25e-01 | 0.257 |
| 2742 | GLRA2 | CRC-3-11773 | Human | Colorectum | CRC | 1.64e-06 | 2.84e-01 | 0.2564 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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:00973051 | Colorectum | MSS | response to alcohol | 66/3467 | 253/18723 | 1.73e-03 | 1.54e-02 | 66 |
| GO:00100382 | Colorectum | MSS | response to metal ion | 90/3467 | 373/18723 | 3.76e-03 | 2.76e-02 | 90 |
| GO:00712412 | Colorectum | MSS | cellular response to inorganic substance | 57/3467 | 226/18723 | 7.27e-03 | 4.64e-02 | 57 |
| GO:00973053 | Colorectum | FAP | response to alcohol | 55/2622 | 253/18723 | 5.05e-04 | 5.78e-03 | 55 |
| GO:0097306 | Colorectum | FAP | cellular response to alcohol | 25/2622 | 93/18723 | 7.87e-04 | 8.29e-03 | 25 |
| GO:00156981 | Colorectum | FAP | inorganic anion transport | 38/2622 | 180/18723 | 5.73e-03 | 3.67e-02 | 38 |
| GO:00100384 | Colorectum | FAP | response to metal ion | 70/2622 | 373/18723 | 5.95e-03 | 3.75e-02 | 70 |
| GO:00973054 | Colorectum | CRC | response to alcohol | 43/2078 | 253/18723 | 2.96e-03 | 2.66e-02 | 43 |
| GO:0042391 | Colorectum | CRC | regulation of membrane potential | 67/2078 | 434/18723 | 3.27e-03 | 2.81e-02 | 67 |
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| 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. |
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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 |
| GLRA2 | SNV | Missense_Mutation | rs777077152 | c.1106N>A | p.Arg369His | p.R369H | P23416 | protein_coding | deleterious(0.04) | probably_damaging(0.991) | TCGA-AQ-A7U7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Targeted Molecular therapy | rituximab | CR |
| GLRA2 | SNV | Missense_Mutation | novel | c.1170N>T | p.Lys390Asn | p.K390N | P23416 | protein_coding | tolerated(0.31) | benign(0.055) | TCGA-AR-A24Z-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| GLRA2 | SNV | Missense_Mutation | c.780N>C | p.Gln260His | p.Q260H | P23416 | protein_coding | deleterious(0.01) | probably_damaging(0.948) | TCGA-BH-A0H7-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| GLRA2 | SNV | Missense_Mutation | c.430N>A | p.Asp144Asn | p.D144N | P23416 | protein_coding | deleterious(0.01) | possibly_damaging(0.492) | TCGA-EW-A1PG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| GLRA2 | SNV | Missense_Mutation | novel | c.52G>A | p.Glu18Lys | p.E18K | P23416 | protein_coding | tolerated_low_confidence(0.48) | possibly_damaging(0.636) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| GLRA2 | SNV | Missense_Mutation | c.169N>A | p.Gly57Arg | p.G57R | P23416 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| GLRA2 | SNV | Missense_Mutation | novel | c.399C>G | p.Phe133Leu | p.F133L | P23416 | protein_coding | deleterious(0) | benign(0.062) | TCGA-C5-A8YQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| GLRA2 | SNV | Missense_Mutation | c.862N>A | p.Ala288Thr | p.A288T | P23416 | protein_coding | deleterious(0.01) | possibly_damaging(0.55) | TCGA-LP-A7HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| GLRA2 | SNV | Missense_Mutation | c.248N>T | p.Gly83Val | p.G83V | P23416 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| GLRA2 | SNV | Missense_Mutation | c.34N>A | p.Leu12Met | p.L12M | P23416 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.86) | TCGA-AA-3821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | 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 |
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | allosteric modulator | 135652747 | ||
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | antagonist | 135651284 | TROPISETRON | |
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | blocker | 135652708 | PICROTOXININ | |
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | blocker | 178101103 | PICROTIN | |
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | blocker | 178100875 | PICROTOXIN | |
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | antagonist | 178101018 | ||
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | antagonist | 135650356 | CHEMBL497392 | |
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | allosteric modulator | 178100984 | ||
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | PICROTOXIN | PICROTOXIN | ||
| 2742 | GLRA2 | DRUGGABLE GENOME, ION CHANNEL | antagonist | 135652718 | STRYCHNINE |
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