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Gene: ABAT |
Gene summary for ABAT |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ABAT | Gene ID | 18 |
| Gene name | 4-aminobutyrate aminotransferase | |
| Gene Alias | GABA-AT | |
| Cytomap | 16p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P80404 |
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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 |
| 18 | ABAT | NAFLD1 | Human | Liver | NAFLD | 3.08e-14 | 9.41e-01 | -0.04 |
| 18 | ABAT | HCC1_Meng | Human | Liver | HCC | 1.36e-10 | -1.21e-01 | 0.0246 |
| 18 | ABAT | HCC1 | Human | Liver | HCC | 5.00e-02 | 2.38e+00 | 0.5336 |
| 18 | ABAT | Pt13.a | Human | Liver | HCC | 9.68e-04 | -1.41e-01 | 0.021 |
| 18 | ABAT | S028 | Human | Liver | HCC | 4.68e-05 | 3.49e-01 | 0.2503 |
| 18 | ABAT | S029 | Human | Liver | HCC | 2.06e-02 | 3.29e-01 | 0.2581 |
| 18 | ABAT | HTA12-26-1 | Human | Pancreas | PDAC | 3.09e-13 | 8.68e-01 | 0.3728 |
| 18 | ABAT | HTA12-29-1 | Human | Pancreas | PDAC | 8.17e-26 | 7.68e-01 | 0.3722 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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:00463953 | Liver | NAFLD | carboxylic acid catabolic process | 73/1882 | 236/18723 | 4.16e-19 | 1.22e-15 | 73 |
| GO:00160544 | Liver | NAFLD | organic acid catabolic process | 73/1882 | 240/18723 | 1.20e-18 | 2.34e-15 | 73 |
| GO:00442825 | Liver | NAFLD | small molecule catabolic process | 91/1882 | 376/18723 | 8.96e-16 | 1.31e-12 | 91 |
| GO:00160535 | Liver | NAFLD | organic acid biosynthetic process | 77/1882 | 316/18723 | 1.03e-13 | 6.69e-11 | 77 |
| GO:00463945 | Liver | NAFLD | carboxylic acid biosynthetic process | 75/1882 | 314/18723 | 6.37e-13 | 3.39e-10 | 75 |
| GO:0009063 | Liver | NAFLD | cellular amino acid catabolic process | 36/1882 | 110/18723 | 6.56e-11 | 1.99e-08 | 36 |
| GO:00610417 | Liver | NAFLD | regulation of wound healing | 39/1882 | 134/18723 | 5.52e-10 | 1.28e-07 | 39 |
| GO:00420607 | Liver | NAFLD | wound healing | 84/1882 | 422/18723 | 6.56e-10 | 1.37e-07 | 84 |
| GO:00065203 | Liver | NAFLD | cellular amino acid metabolic process | 63/1882 | 284/18723 | 1.14e-09 | 2.17e-07 | 63 |
| GO:0030195 | Liver | NAFLD | negative regulation of blood coagulation | 21/1882 | 49/18723 | 2.42e-09 | 4.05e-07 | 21 |
| GO:00094107 | Liver | NAFLD | response to xenobiotic stimulus | 88/1882 | 462/18723 | 2.53e-09 | 4.11e-07 | 88 |
| GO:1900047 | Liver | NAFLD | negative regulation of hemostasis | 21/1882 | 50/18723 | 3.78e-09 | 5.40e-07 | 21 |
| GO:0030193 | Liver | NAFLD | regulation of blood coagulation | 24/1882 | 66/18723 | 9.30e-09 | 1.26e-06 | 24 |
| GO:00086523 | Liver | NAFLD | cellular amino acid biosynthetic process | 26/1882 | 76/18723 | 1.00e-08 | 1.33e-06 | 26 |
| GO:0050819 | Liver | NAFLD | negative regulation of coagulation | 21/1882 | 53/18723 | 1.33e-08 | 1.69e-06 | 21 |
| GO:1900046 | Liver | NAFLD | regulation of hemostasis | 24/1882 | 68/18723 | 1.84e-08 | 2.09e-06 | 24 |
| GO:0061045 | Liver | NAFLD | negative regulation of wound healing | 26/1882 | 78/18723 | 1.86e-08 | 2.09e-06 | 26 |
| GO:19030347 | Liver | NAFLD | regulation of response to wounding | 41/1882 | 167/18723 | 4.70e-08 | 4.58e-06 | 41 |
| GO:0050818 | Liver | NAFLD | regulation of coagulation | 24/1882 | 71/18723 | 4.80e-08 | 4.60e-06 | 24 |
| GO:00075994 | Liver | NAFLD | hemostasis | 49/1882 | 222/18723 | 9.23e-08 | 7.59e-06 | 49 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0028041 | Liver | HCC | Valine, leucine and isoleucine degradation | 41/4020 | 48/8465 | 4.84e-08 | 7.05e-07 | 3.92e-07 | 41 |
| hsa0064041 | Liver | HCC | Propanoate metabolism | 24/4020 | 32/8465 | 1.42e-03 | 5.07e-03 | 2.82e-03 | 24 |
| hsa006504 | Liver | HCC | Butanoate metabolism | 19/4020 | 27/8465 | 1.37e-02 | 3.33e-02 | 1.85e-02 | 19 |
| hsa0028051 | Liver | HCC | Valine, leucine and isoleucine degradation | 41/4020 | 48/8465 | 4.84e-08 | 7.05e-07 | 3.92e-07 | 41 |
| hsa0064051 | Liver | HCC | Propanoate metabolism | 24/4020 | 32/8465 | 1.42e-03 | 5.07e-03 | 2.82e-03 | 24 |
| hsa006505 | Liver | HCC | Butanoate metabolism | 19/4020 | 27/8465 | 1.37e-02 | 3.33e-02 | 1.85e-02 | 19 |
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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 |
| ABAT | SNV | Missense_Mutation | c.74N>G | p.Ser25Cys | p.S25C | P80404 | protein_coding | tolerated(0.18) | benign(0) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| ABAT | SNV | Missense_Mutation | c.583N>A | p.Glu195Lys | p.E195K | P80404 | protein_coding | tolerated(0.18) | benign(0.103) | TCGA-AN-A0FW-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| ABAT | SNV | Missense_Mutation | c.1080N>A | p.Met360Ile | p.M360I | P80404 | protein_coding | tolerated(0.32) | benign(0.006) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| ABAT | SNV | Missense_Mutation | c.10N>G | p.Met4Val | p.M4V | P80404 | protein_coding | tolerated_low_confidence(1) | benign(0) | TCGA-BH-A0GY-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyotxan | SD | |
| ABAT | SNV | Missense_Mutation | rs762137050 | c.1424N>A | p.Arg475His | p.R475H | P80404 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-HN-A2NL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| ABAT | insertion | In_Frame_Ins | novel | c.426_427insCAGGCA | p.Lys142_Leu143insGlnAla | p.K142_L143insQA | P80404 | protein_coding | TCGA-AO-A03P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | PD | ||
| ABAT | insertion | Frame_Shift_Ins | novel | c.428_429insGCACTCTGCCTGTTTTTTAG | p.Arg144HisfsTer36 | p.R144Hfs*36 | P80404 | protein_coding | TCGA-AO-A03P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | PD | ||
| ABAT | SNV | Missense_Mutation | novel | c.892G>A | p.Glu298Lys | p.E298K | P80404 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A1MP-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| ABAT | SNV | Missense_Mutation | rs752701740 | c.205N>C | p.Glu69Gln | p.E69Q | P80404 | protein_coding | tolerated(0.29) | benign(0.104) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ABAT | SNV | Missense_Mutation | c.766N>A | p.Glu256Lys | p.E256K | P80404 | protein_coding | deleterious(0.01) | possibly_damaging(0.798) | TCGA-AA-3688-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | 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 |
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | valproic acid | 23407051 | ||
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | Divalproex sodium | |||
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | Pyridoxal Phosphate | |||
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | DIVALPROEX SODIUM | |||
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | inhibitor | 178101523 | VIGABATRIN | |
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | CPP -15 | |||
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | 4-hydroxybenzaldehyde | 4-HYDROXYBENZALDEHYDE | ||
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | L-Alanine | L-ALANINE | ||
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | TIAGABINE | TIAGABINE | ||
| 18 | ABAT | DRUGGABLE GENOME, ENZYME | Pyruvic acid |
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