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Gene: GABRB3 |
Gene summary for GABRB3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GABRB3 | Gene ID | 2562 |
| Gene name | gamma-aminobutyric acid type A receptor subunit beta3 | |
| Gene Alias | DEE43 | |
| Cytomap | 15q12 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | P28472 |
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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 |
| 2562 | GABRB3 | HTA11_696_2000001011 | Human | Colorectum | AD | 8.37e-03 | 9.21e-02 | -0.1464 |
| 2562 | GABRB3 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.26e-03 | 1.10e-01 | -0.1001 |
| 2562 | GABRB3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.30e-03 | 2.49e-01 | -0.059 |
| 2562 | GABRB3 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.97e-02 | 1.17e-01 | 0.096 |
| 2562 | GABRB3 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.54e-04 | 2.11e-01 | 0.0588 |
| 2562 | GABRB3 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 8.41e-03 | 6.23e-01 | 0.3487 |
| 2562 | GABRB3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.89e-13 | 3.84e-01 | 0.3859 |
| 2562 | GABRB3 | P2T-E | Human | Esophagus | ESCC | 9.56e-08 | 1.53e-01 | 0.1177 |
| 2562 | GABRB3 | P9T-E | Human | Esophagus | ESCC | 2.17e-02 | 1.22e-01 | 0.1131 |
| 2562 | GABRB3 | P10T-E | Human | Esophagus | ESCC | 7.31e-14 | 2.33e-01 | 0.116 |
| 2562 | GABRB3 | P16T-E | Human | Esophagus | ESCC | 1.14e-02 | 2.26e-02 | 0.1153 |
| 2562 | GABRB3 | P22T-E | Human | Esophagus | ESCC | 3.60e-13 | 2.54e-01 | 0.1236 |
| 2562 | GABRB3 | P39T-E | Human | Esophagus | ESCC | 1.88e-04 | 1.32e-01 | 0.0894 |
| 2562 | GABRB3 | P49T-E | Human | Esophagus | ESCC | 1.19e-05 | 5.39e-01 | 0.1768 |
| 2562 | GABRB3 | P76T-E | Human | Esophagus | ESCC | 1.88e-04 | 1.17e-01 | 0.1207 |
| 2562 | GABRB3 | P79T-E | Human | Esophagus | ESCC | 1.66e-02 | 9.43e-02 | 0.1154 |
| 2562 | GABRB3 | P83T-E | Human | Esophagus | ESCC | 3.46e-03 | 1.89e-01 | 0.1738 |
| 2562 | GABRB3 | P127T-E | Human | Esophagus | ESCC | 1.76e-03 | 7.79e-02 | 0.0826 |
| 2562 | GABRB3 | P128T-E | Human | Esophagus | ESCC | 1.54e-07 | 2.63e-01 | 0.1241 |
| 2562 | GABRB3 | P130T-E | Human | Esophagus | ESCC | 1.59e-30 | 5.49e-01 | 0.1676 |
| Page: 1 2 |
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias |
| ∗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:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
| GO:0050808 | Colorectum | AD | synapse organization | 112/3918 | 426/18723 | 4.25e-03 | 2.92e-02 | 112 |
| GO:0015698 | Colorectum | AD | inorganic anion transport | 52/3918 | 180/18723 | 6.83e-03 | 4.22e-02 | 52 |
| GO:00343292 | Colorectum | MSS | cell junction assembly | 120/3467 | 420/18723 | 2.51e-07 | 1.07e-05 | 120 |
| GO:00508082 | Colorectum | MSS | synapse organization | 101/3467 | 426/18723 | 3.96e-03 | 2.89e-02 | 101 |
| GO:003432918 | Esophagus | ESCC | cell junction assembly | 227/8552 | 420/18723 | 3.06e-04 | 1.83e-03 | 227 |
| GO:0060021 | Esophagus | ESCC | roof of mouth development | 50/8552 | 85/18723 | 1.00e-02 | 3.42e-02 | 50 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04723 | Colorectum | AD | Retrograde endocannabinoid signaling | 59/2092 | 148/8465 | 2.94e-05 | 2.73e-04 | 1.74e-04 | 59 |
| hsa047231 | Colorectum | AD | Retrograde endocannabinoid signaling | 59/2092 | 148/8465 | 2.94e-05 | 2.73e-04 | 1.74e-04 | 59 |
| hsa047234 | Colorectum | MSS | Retrograde endocannabinoid signaling | 61/1875 | 148/8465 | 1.21e-07 | 1.93e-06 | 1.18e-06 | 61 |
| hsa047235 | Colorectum | MSS | Retrograde endocannabinoid signaling | 61/1875 | 148/8465 | 1.21e-07 | 1.93e-06 | 1.18e-06 | 61 |
| hsa047236 | Colorectum | MSI-H | Retrograde endocannabinoid signaling | 33/797 | 148/8465 | 1.88e-06 | 3.21e-05 | 2.69e-05 | 33 |
| hsa047237 | Colorectum | MSI-H | Retrograde endocannabinoid signaling | 33/797 | 148/8465 | 1.88e-06 | 3.21e-05 | 2.69e-05 | 33 |
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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 |
| GABRB3 | SNV | Missense_Mutation | c.570N>T | p.Glu190Asp | p.E190D | P28472 | protein_coding | tolerated(0.45) | possibly_damaging(0.449) | TCGA-A8-A09A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| GABRB3 | SNV | Missense_Mutation | c.340N>A | p.Asp114Asn | p.D114N | P28472 | protein_coding | deleterious(0.04) | possibly_damaging(0.838) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| GABRB3 | SNV | Missense_Mutation | c.187G>T | p.Val63Leu | p.V63L | P28472 | protein_coding | tolerated(0.1) | possibly_damaging(0.78) | TCGA-E9-A295-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| GABRB3 | insertion | Nonsense_Mutation | novel | c.901_902insTATTGAGAAGTGGAGTGCATTCTTGAATTTGGGTGAGGGCATTTGGA | p.Pro301LeufsTer9 | p.P301Lfs*9 | P28472 | protein_coding | TCGA-A8-A06Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD | ||
| GABRB3 | insertion | Nonsense_Mutation | novel | c.626_627insTTAGTGG | p.Gln210Ter | p.Q210* | P28472 | protein_coding | TCGA-B6-A0IB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| GABRB3 | insertion | Nonsense_Mutation | novel | c.625_626insACTGGGGTTAGCAGCCAGC | p.Pro209HisfsTer4 | p.P209Hfs*4 | P28472 | protein_coding | TCGA-B6-A0IB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| GABRB3 | SNV | Missense_Mutation | novel | c.181N>A | p.Val61Ile | p.V61I | P28472 | protein_coding | tolerated(0.07) | possibly_damaging(0.644) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| GABRB3 | SNV | Missense_Mutation | c.1024N>A | p.Leu342Ile | p.L342I | P28472 | protein_coding | tolerated(0.3) | benign(0.007) | TCGA-EA-A5ZD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| GABRB3 | SNV | Missense_Mutation | c.835N>A | p.Gly279Arg | p.G279R | P28472 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-FU-A23K-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| GABRB3 | SNV | Missense_Mutation | rs766672883 | c.1330N>A | p.Asp444Asn | p.D444N | P28472 | protein_coding | deleterious(0.03) | possibly_damaging(0.514) | TCGA-FU-A23L-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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 |
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | positive modulator | CHEMBL2096631 | CLORAZEPATE DIPOTASSIUM | |
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | CHEMBL591 | ETHCHLORVYNOL | ||
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | PROPOFOL | PROPOFOL | ||
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | positive modulator | CHEMBL1200602 | ||
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | CLORAZEPATE | CLORAZEPIC ACID | ||
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | CLOTIAZEPAM | CLOTIAZEPAM | ||
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | CHEMBL2068724 | ACAMPROSATE CALCIUM | ||
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | positive modulator | CHEMBL450 | METHARBITAL | |
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | CHEMBL1102 | GLUTETHIMIDE | ||
| 2562 | GABRB3 | ION CHANNEL, DRUGGABLE GENOME | EVT-201 |
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