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Gene: AGXT |
Gene summary for AGXT |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | AGXT | Gene ID | 189 |
| Gene name | alanine--glyoxylate and serine--pyruvate aminotransferase | |
| Gene Alias | AGT | |
| Cytomap | 2q37.3 | |
| Gene Type | protein-coding | GO ID | GO:0000096 | UniProtAcc | P21549 |
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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 |
| 189 | AGXT | NAFLD1 | Human | Liver | NAFLD | 3.15e-11 | 1.03e+00 | -0.04 |
| 189 | AGXT | S41 | Human | Liver | Cirrhotic | 1.72e-02 | 3.45e-01 | -0.0343 |
| 189 | AGXT | S43 | Human | Liver | Cirrhotic | 2.75e-06 | -1.20e-01 | -0.0187 |
| 189 | AGXT | HCC1_Meng | Human | Liver | HCC | 3.07e-67 | -1.75e-01 | 0.0246 |
| 189 | AGXT | HCC2_Meng | Human | Liver | HCC | 1.09e-11 | -3.75e-01 | 0.0107 |
| 189 | AGXT | cirrhotic1 | Human | Liver | Cirrhotic | 3.53e-09 | -3.20e-01 | 0.0202 |
| 189 | AGXT | cirrhotic2 | Human | Liver | Cirrhotic | 1.31e-07 | -2.82e-01 | 0.0201 |
| 189 | AGXT | HCC2 | Human | Liver | HCC | 2.58e-44 | 5.72e+00 | 0.5341 |
| 189 | AGXT | Pt13.a | Human | Liver | HCC | 7.05e-11 | 1.70e-01 | 0.021 |
| 189 | AGXT | Pt13.b | Human | Liver | HCC | 1.54e-43 | 2.44e-01 | 0.0251 |
| 189 | AGXT | Pt14.b | Human | Liver | HCC | 1.89e-12 | 3.23e-01 | 0.018 |
| 189 | AGXT | Pt14.d | Human | Liver | HCC | 3.16e-06 | 1.13e-02 | 0.0143 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00723295 | Liver | NAFLD | monocarboxylic acid catabolic process | 39/1882 | 122/18723 | 2.40e-11 | 8.77e-09 | 39 |
| GO:00485457 | Liver | NAFLD | response to steroid hormone | 75/1882 | 339/18723 | 3.44e-11 | 1.12e-08 | 75 |
| GO:0009063 | Liver | NAFLD | cellular amino acid catabolic process | 36/1882 | 110/18723 | 6.56e-11 | 1.99e-08 | 36 |
| GO:00065203 | Liver | NAFLD | cellular amino acid metabolic process | 63/1882 | 284/18723 | 1.14e-09 | 2.17e-07 | 63 |
| GO:00086523 | Liver | NAFLD | cellular amino acid biosynthetic process | 26/1882 | 76/18723 | 1.00e-08 | 1.33e-06 | 26 |
| GO:19016053 | Liver | NAFLD | alpha-amino acid metabolic process | 46/1882 | 195/18723 | 2.74e-08 | 2.86e-06 | 46 |
| GO:00513846 | Liver | NAFLD | response to glucocorticoid | 36/1882 | 148/18723 | 3.88e-07 | 2.52e-05 | 36 |
| GO:19016073 | Liver | NAFLD | alpha-amino acid biosynthetic process | 22/1882 | 68/18723 | 4.13e-07 | 2.62e-05 | 22 |
| GO:00723303 | Liver | NAFLD | monocarboxylic acid biosynthetic process | 46/1882 | 214/18723 | 5.06e-07 | 3.07e-05 | 46 |
| GO:1901606 | Liver | NAFLD | alpha-amino acid catabolic process | 25/1882 | 87/18723 | 8.67e-07 | 4.60e-05 | 25 |
| GO:00319606 | Liver | NAFLD | response to corticosteroid | 37/1882 | 167/18723 | 3.03e-06 | 1.23e-04 | 37 |
| GO:00060907 | Liver | NAFLD | pyruvate metabolic process | 26/1882 | 106/18723 | 1.31e-05 | 3.93e-04 | 26 |
| GO:00067904 | Liver | NAFLD | sulfur compound metabolic process | 58/1882 | 339/18723 | 3.79e-05 | 9.38e-04 | 58 |
| GO:0000096 | Liver | NAFLD | sulfur amino acid metabolic process | 12/1882 | 34/18723 | 6.82e-05 | 1.45e-03 | 12 |
| GO:00466837 | Liver | NAFLD | response to organophosphorus | 28/1882 | 131/18723 | 9.05e-05 | 1.82e-03 | 28 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0120010 | Liver | NAFLD | Carbon metabolism | 26/1043 | 115/8465 | 1.39e-03 | 1.71e-02 | 1.38e-02 | 26 |
| hsa04146 | Liver | NAFLD | Peroxisome | 19/1043 | 82/8465 | 4.37e-03 | 4.10e-02 | 3.30e-02 | 19 |
| hsa0120011 | Liver | NAFLD | Carbon metabolism | 26/1043 | 115/8465 | 1.39e-03 | 1.71e-02 | 1.38e-02 | 26 |
| hsa041461 | Liver | NAFLD | Peroxisome | 19/1043 | 82/8465 | 4.37e-03 | 4.10e-02 | 3.30e-02 | 19 |
| hsa041462 | Liver | Cirrhotic | Peroxisome | 36/2530 | 82/8465 | 4.79e-03 | 1.74e-02 | 1.07e-02 | 36 |
| hsa041463 | Liver | Cirrhotic | Peroxisome | 36/2530 | 82/8465 | 4.79e-03 | 1.74e-02 | 1.07e-02 | 36 |
| hsa0120041 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
| hsa041464 | Liver | HCC | Peroxisome | 58/4020 | 82/8465 | 1.57e-05 | 1.05e-04 | 5.85e-05 | 58 |
| hsa0063021 | Liver | HCC | Glyoxylate and dicarboxylate metabolism | 24/4020 | 30/8465 | 2.66e-04 | 1.24e-03 | 6.88e-04 | 24 |
| hsa002602 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
| hsa0120051 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
| hsa041465 | Liver | HCC | Peroxisome | 58/4020 | 82/8465 | 1.57e-05 | 1.05e-04 | 5.85e-05 | 58 |
| hsa0063031 | Liver | HCC | Glyoxylate and dicarboxylate metabolism | 24/4020 | 30/8465 | 2.66e-04 | 1.24e-03 | 6.88e-04 | 24 |
| hsa002603 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
| Page: 1 |
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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 |
| AGXT | SNV | Missense_Mutation | rs375712696 | c.31N>G | p.Pro11Ala | p.P11A | P21549 | protein_coding | deleterious(0) | probably_damaging(0.956) | TCGA-C8-A12K-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| AGXT | insertion | Frame_Shift_Ins | novel | c.217_218insGTTTCTGGTATTGCAGAAATCATAGT | p.Pro73ArgfsTer56 | p.P73Rfs*56 | P21549 | protein_coding | TCGA-A7-A0D9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | ||
| AGXT | SNV | Missense_Mutation | rs758493460 | c.1078C>T | p.Arg360Trp | p.R360W | P21549 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| AGXT | SNV | Missense_Mutation | c.236C>G | p.Ser79Cys | p.S79C | P21549 | protein_coding | deleterious(0.01) | possibly_damaging(0.517) | TCGA-EK-A2R8-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| AGXT | SNV | Missense_Mutation | rs761622783 | c.877N>A | p.Glu293Lys | p.E293K | P21549 | protein_coding | tolerated(0.33) | benign(0.056) | TCGA-MA-AA42-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| AGXT | deletion | Frame_Shift_Del | rs768991178 | c.26delN | p.Lys12ArgfsTer34 | p.K12Rfs*34 | P21549 | protein_coding | TCGA-MA-AA42-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| AGXT | SNV | Missense_Mutation | c.881N>T | p.Ala294Val | p.A294V | P21549 | protein_coding | tolerated(1) | benign(0.001) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| AGXT | insertion | Frame_Shift_Ins | rs777193616 | c.33dupC | p.Lys12GlnfsTer156 | p.K12Qfs*156 | P21549 | protein_coding | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| AGXT | deletion | Frame_Shift_Del | rs768991178 | c.26delN | p.Lys12ArgfsTer34 | p.K12Rfs*34 | P21549 | protein_coding | TCGA-CK-5913-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| AGXT | insertion | Frame_Shift_Ins | rs777193616 | c.33dupC | p.Lys12GlnfsTer156 | p.K12Qfs*156 | P21549 | protein_coding | TCGA-D5-6530-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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