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Gene: SLC38A1 |
Gene summary for SLC38A1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SLC38A1 | Gene ID | 81539 |
| Gene name | solute carrier family 38 member 1 | |
| Gene Alias | ATA1 | |
| Cytomap | 12q13.11 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A024R124 |
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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 |
| 81539 | SLC38A1 | GSM4909286 | Human | Breast | IDC | 7.45e-04 | -3.06e-01 | 0.1081 |
| 81539 | SLC38A1 | GSM4909291 | Human | Breast | IDC | 6.50e-07 | 4.83e-01 | 0.1753 |
| 81539 | SLC38A1 | GSM4909292 | Human | Breast | IDC | 5.21e-03 | 6.30e-01 | 0.1236 |
| 81539 | SLC38A1 | GSM4909293 | Human | Breast | IDC | 3.56e-18 | 3.68e-01 | 0.1581 |
| 81539 | SLC38A1 | GSM4909296 | Human | Breast | IDC | 3.42e-06 | -2.82e-01 | 0.1524 |
| 81539 | SLC38A1 | GSM4909297 | Human | Breast | IDC | 3.40e-03 | -1.78e-01 | 0.1517 |
| 81539 | SLC38A1 | GSM4909298 | Human | Breast | IDC | 2.23e-02 | 1.67e-01 | 0.1551 |
| 81539 | SLC38A1 | GSM4909302 | Human | Breast | IDC | 1.35e-22 | 6.93e-01 | 0.1545 |
| 81539 | SLC38A1 | GSM4909303 | Human | Breast | IDC | 7.99e-04 | 4.77e-01 | 0.0438 |
| 81539 | SLC38A1 | GSM4909304 | Human | Breast | IDC | 9.04e-19 | 5.26e-01 | 0.1636 |
| 81539 | SLC38A1 | GSM4909306 | Human | Breast | IDC | 1.63e-03 | 2.41e-01 | 0.1564 |
| 81539 | SLC38A1 | GSM4909307 | Human | Breast | IDC | 1.88e-10 | -3.68e-01 | 0.1569 |
| 81539 | SLC38A1 | GSM4909308 | Human | Breast | IDC | 1.93e-15 | -4.20e-01 | 0.158 |
| 81539 | SLC38A1 | GSM4909311 | Human | Breast | IDC | 1.75e-14 | -2.66e-01 | 0.1534 |
| 81539 | SLC38A1 | GSM4909312 | Human | Breast | IDC | 1.69e-02 | 5.24e-02 | 0.1552 |
| 81539 | SLC38A1 | GSM4909317 | Human | Breast | IDC | 1.81e-06 | 4.02e-01 | 0.1355 |
| 81539 | SLC38A1 | GSM4909319 | Human | Breast | IDC | 6.13e-20 | -2.79e-01 | 0.1563 |
| 81539 | SLC38A1 | GSM4909321 | Human | Breast | IDC | 2.24e-03 | -1.09e-01 | 0.1559 |
| 81539 | SLC38A1 | brca2 | Human | Breast | Precancer | 3.25e-03 | 8.57e-02 | -0.024 |
| 81539 | SLC38A1 | brca3 | Human | Breast | Precancer | 1.73e-02 | 9.88e-02 | -0.0263 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00075653 | Breast | Precancer | female pregnancy | 29/1080 | 193/18723 | 2.07e-06 | 7.31e-05 | 29 |
| GO:00447063 | Breast | Precancer | multi-multicellular organism process | 31/1080 | 220/18723 | 3.73e-06 | 1.19e-04 | 31 |
| GO:000756511 | Breast | IDC | female pregnancy | 39/1434 | 193/18723 | 1.81e-08 | 1.27e-06 | 39 |
| GO:00447061 | Breast | IDC | multi-multicellular organism process | 41/1434 | 220/18723 | 8.58e-08 | 5.19e-06 | 41 |
| GO:00075652 | Breast | DCIS | female pregnancy | 37/1390 | 193/18723 | 7.85e-08 | 4.47e-06 | 37 |
| GO:00447062 | Breast | DCIS | multi-multicellular organism process | 39/1390 | 220/18723 | 3.05e-07 | 1.46e-05 | 39 |
| GO:0150104 | Colorectum | MSS | transport across blood-brain barrier | 28/3467 | 87/18723 | 1.54e-03 | 1.41e-02 | 28 |
| GO:0010232 | Colorectum | MSS | vascular transport | 28/3467 | 88/18723 | 1.87e-03 | 1.64e-02 | 28 |
| GO:01501041 | Colorectum | FAP | transport across blood-brain barrier | 25/2622 | 87/18723 | 2.63e-04 | 3.59e-03 | 25 |
| GO:00102321 | Colorectum | FAP | vascular transport | 25/2622 | 88/18723 | 3.19e-04 | 4.12e-03 | 25 |
| GO:0006814 | Colorectum | FAP | sodium ion transport | 54/2622 | 245/18723 | 3.98e-04 | 4.85e-03 | 54 |
| GO:0003018 | Colorectum | FAP | vascular process in circulatory system | 56/2622 | 263/18723 | 7.67e-04 | 8.12e-03 | 56 |
| GO:00068141 | Colorectum | CRC | sodium ion transport | 49/2078 | 245/18723 | 3.01e-05 | 7.86e-04 | 49 |
| GO:00030181 | Colorectum | CRC | vascular process in circulatory system | 45/2078 | 263/18723 | 2.10e-03 | 2.08e-02 | 45 |
| GO:01501042 | Colorectum | CRC | transport across blood-brain barrier | 18/2078 | 87/18723 | 6.50e-03 | 4.69e-02 | 18 |
| GO:00075655 | Endometrium | AEH | female pregnancy | 43/2100 | 193/18723 | 7.52e-06 | 1.80e-04 | 43 |
| GO:00447065 | Endometrium | AEH | multi-multicellular organism process | 45/2100 | 220/18723 | 4.55e-05 | 7.61e-04 | 45 |
| GO:000756513 | Endometrium | EEC | female pregnancy | 43/2168 | 193/18723 | 1.66e-05 | 3.18e-04 | 43 |
| GO:004470612 | Endometrium | EEC | multi-multicellular organism process | 45/2168 | 220/18723 | 9.73e-05 | 1.35e-03 | 45 |
| GO:00603485 | Esophagus | ESCC | bone development | 115/8552 | 205/18723 | 1.67e-03 | 7.72e-03 | 115 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04724 | Colorectum | CRC | Glutamatergic synapse | 24/1091 | 115/8465 | 1.07e-02 | 4.74e-02 | 3.21e-02 | 24 |
| hsa047241 | Colorectum | CRC | Glutamatergic synapse | 24/1091 | 115/8465 | 1.07e-02 | 4.74e-02 | 3.21e-02 | 24 |
| 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 |
| SLC38A1 | SNV | Missense_Mutation | novel | c.1174N>G | p.Arg392Gly | p.R392G | protein_coding | deleterious(0) | possibly_damaging(0.794) | TCGA-A8-A09A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| SLC38A1 | SNV | Missense_Mutation | rs767003327 | c.584N>A | p.Arg195His | p.R195H | protein_coding | deleterious(0.01) | benign(0.3) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SLC38A1 | SNV | Missense_Mutation | c.1332G>C | p.Gln444His | p.Q444H | protein_coding | deleterious(0.01) | possibly_damaging(0.54) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | ||
| SLC38A1 | insertion | Frame_Shift_Ins | novel | c.1392_1393insATTTC | p.Phe465IlefsTer66 | p.F465Ifs*66 | Q9H2H9 | protein_coding | TCGA-BH-A0HK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| SLC38A1 | insertion | Nonsense_Mutation | novel | c.1390_1391insAGAGAAAGAAATGTCTGAGAAATAGTTCCCT | p.Leu464Ter | p.L464* | Q9H2H9 | protein_coding | TCGA-BH-A0HK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| SLC38A1 | SNV | Missense_Mutation | c.510A>C | p.Lys170Asn | p.K170N | protein_coding | deleterious(0.01) | probably_damaging(0.914) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
| SLC38A1 | SNV | Missense_Mutation | novel | c.1309C>G | p.Leu437Val | p.L437V | protein_coding | deleterious(0) | possibly_damaging(0.491) | TCGA-VS-A9U5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| SLC38A1 | SNV | Missense_Mutation | novel | c.1156N>G | p.Thr386Ala | p.T386A | protein_coding | tolerated(0.8) | benign(0.088) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SLC38A1 | SNV | Missense_Mutation | novel | c.28T>A | p.Leu10Ile | p.L10I | protein_coding | tolerated_low_confidence(0.22) | benign(0.419) | TCGA-AA-A01D-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | capecitabine | PD | |
| SLC38A1 | SNV | Missense_Mutation | c.1070N>T | p.Arg357Leu | p.R357L | protein_coding | deleterious(0) | probably_damaging(0.943) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
| 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 |
| 81539 | SLC38A1 | TRANSPORTER | 178101263 | |||
| 81539 | SLC38A1 | TRANSPORTER | 178101264 |
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