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Gene: SLC28A2 |
Gene summary for SLC28A2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SLC28A2 | Gene ID | 9153 |
| Gene name | solute carrier family 28 member 2 | |
| Gene Alias | CNT2 | |
| Cytomap | 15q21.1 | |
| Gene Type | protein-coding | GO ID | GO:0001894 | UniProtAcc | O43868 |
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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 |
| 9153 | SLC28A2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 8.14e-04 | -3.36e-01 | -0.1808 |
| 9153 | SLC28A2 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.02e-30 | 1.17e+00 | -0.1954 |
| 9153 | SLC28A2 | HTA11_866_3004761011 | Human | Colorectum | AD | 6.82e-03 | -3.01e-01 | 0.096 |
| 9153 | SLC28A2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.15e-05 | -3.84e-01 | 0.0338 |
| 9153 | SLC28A2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.25e-05 | -2.96e-01 | 0.0674 |
| 9153 | SLC28A2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.52e-05 | -3.95e-01 | 0.0588 |
| 9153 | SLC28A2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.37e-06 | -3.95e-01 | 0.281 |
| 9153 | SLC28A2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.18e-18 | -3.88e-01 | 0.3859 |
| 9153 | SLC28A2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.53e-02 | -3.79e-01 | 0.2585 |
| 9153 | SLC28A2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.44e-19 | -3.95e-01 | 0.3005 |
| 9153 | SLC28A2 | F007 | Human | Colorectum | FAP | 2.47e-08 | -3.95e-01 | 0.1176 |
| 9153 | SLC28A2 | A002-C-010 | Human | Colorectum | FAP | 2.22e-03 | -2.50e-01 | 0.242 |
| 9153 | SLC28A2 | A015-C-203 | Human | Colorectum | FAP | 9.28e-13 | -2.58e-01 | -0.1294 |
| 9153 | SLC28A2 | A015-C-204 | Human | Colorectum | FAP | 1.30e-03 | -2.82e-01 | -0.0228 |
| 9153 | SLC28A2 | A002-C-201 | Human | Colorectum | FAP | 3.58e-06 | -2.65e-01 | 0.0324 |
| 9153 | SLC28A2 | A002-C-203 | Human | Colorectum | FAP | 3.26e-19 | -3.92e-01 | 0.2786 |
| 9153 | SLC28A2 | A001-C-119 | Human | Colorectum | FAP | 2.67e-07 | -3.74e-01 | -0.1557 |
| 9153 | SLC28A2 | A001-C-108 | Human | Colorectum | FAP | 3.78e-09 | -2.54e-01 | -0.0272 |
| 9153 | SLC28A2 | A002-C-205 | Human | Colorectum | FAP | 5.27e-13 | -3.68e-01 | -0.1236 |
| 9153 | SLC28A2 | A015-C-006 | Human | Colorectum | FAP | 9.13e-07 | -3.35e-01 | -0.0994 |
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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 | ||
| 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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0015931 | Colorectum | AD | nucleobase-containing compound transport | 73/3918 | 222/18723 | 2.02e-05 | 4.10e-04 | 73 |
| GO:0060249 | Colorectum | AD | anatomical structure homeostasis | 94/3918 | 314/18723 | 9.37e-05 | 1.42e-03 | 94 |
| GO:0001894 | Colorectum | AD | tissue homeostasis | 81/3918 | 268/18723 | 1.96e-04 | 2.62e-03 | 81 |
| GO:00018941 | Colorectum | SER | tissue homeostasis | 66/2897 | 268/18723 | 5.87e-05 | 1.37e-03 | 66 |
| GO:00602491 | Colorectum | SER | anatomical structure homeostasis | 74/2897 | 314/18723 | 1.01e-04 | 2.13e-03 | 74 |
| GO:00159311 | Colorectum | SER | nucleobase-containing compound transport | 54/2897 | 222/18723 | 3.65e-04 | 5.67e-03 | 54 |
| GO:00159312 | Colorectum | MSS | nucleobase-containing compound transport | 70/3467 | 222/18723 | 1.92e-06 | 6.01e-05 | 70 |
| GO:00602492 | Colorectum | MSS | anatomical structure homeostasis | 84/3467 | 314/18723 | 1.87e-04 | 2.64e-03 | 84 |
| GO:00018942 | Colorectum | MSS | tissue homeostasis | 72/3467 | 268/18723 | 4.53e-04 | 5.40e-03 | 72 |
| 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:00018944 | Colorectum | FAP | tissue homeostasis | 61/2622 | 268/18723 | 6.71e-05 | 1.28e-03 | 61 |
| GO:00602494 | Colorectum | FAP | anatomical structure homeostasis | 69/2622 | 314/18723 | 7.51e-05 | 1.37e-03 | 69 |
| 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:0003018 | Colorectum | FAP | vascular process in circulatory system | 56/2622 | 263/18723 | 7.67e-04 | 8.12e-03 | 56 |
| GO:00159314 | Colorectum | FAP | nucleobase-containing compound transport | 45/2622 | 222/18723 | 6.22e-03 | 3.90e-02 | 45 |
| GO:00602495 | Colorectum | CRC | anatomical structure homeostasis | 57/2078 | 314/18723 | 1.24e-04 | 2.41e-03 | 57 |
| GO:00018945 | Colorectum | CRC | tissue homeostasis | 48/2078 | 268/18723 | 5.56e-04 | 7.70e-03 | 48 |
| GO:00030181 | Colorectum | CRC | vascular process in circulatory system | 45/2078 | 263/18723 | 2.10e-03 | 2.08e-02 | 45 |
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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 |
| SLC28A2 | SNV | Missense_Mutation | c.923G>C | p.Gly308Ala | p.G308A | O43868 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A7-A426-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| SLC28A2 | SNV | Missense_Mutation | rs767103219 | c.1336G>A | p.Glu446Lys | p.E446K | O43868 | protein_coding | tolerated(0.2) | possibly_damaging(0.544) | TCGA-A8-A099-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD |
| SLC28A2 | SNV | Missense_Mutation | novel | c.491N>T | p.Ala164Val | p.A164V | O43868 | protein_coding | tolerated(0.85) | benign(0.007) | TCGA-E2-A14R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
| SLC28A2 | SNV | Missense_Mutation | c.175N>C | p.Ser59Arg | p.S59R | O43868 | protein_coding | tolerated(0.57) | benign(0.001) | TCGA-E2-A150-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| SLC28A2 | insertion | Frame_Shift_Ins | novel | c.570_571insAGGGCTAAAAGGAGTAGTTACCCTGTGACTCTTTCTTTGAGGG | p.Ser191ArgfsTer44 | p.S191Rfs*44 | O43868 | protein_coding | TCGA-AN-A0FS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SLC28A2 | deletion | Frame_Shift_Del | novel | c.1735delN | p.Ala579ProfsTer45 | p.A579Pfs*45 | O43868 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| SLC28A2 | SNV | Missense_Mutation | novel | c.1430N>T | p.Cys477Phe | p.C477F | O43868 | protein_coding | deleterious(0.02) | probably_damaging(0.943) | TCGA-EA-A439-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| SLC28A2 | SNV | Missense_Mutation | rs759432504 | c.1170G>C | p.Lys390Asn | p.K390N | O43868 | protein_coding | tolerated(0.09) | possibly_damaging(0.77) | TCGA-MU-A8JM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| SLC28A2 | SNV | Missense_Mutation | c.1368G>T | p.Gln456His | p.Q456H | O43868 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| SLC28A2 | SNV | Missense_Mutation | novel | c.895A>T | p.Thr299Ser | p.T299S | O43868 | protein_coding | tolerated(0.99) | benign(0.402) | TCGA-AA-3930-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | PD |
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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 |
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | ADENOSINE | ADENOSINE | 23388705 | |
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | tenofovir disoproxil fumarate | 31619748 | ||
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | URIDINE | URIDINE | 11641443 | |
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | gemcitabine | GEMCITABINE | 18538445,20665488 | |
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | URIDINE | URIDINE | 23388705 | |
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | ribavirin | RIBAVIRIN | 26071337 | |
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | peginterferon alfa-2b | 26071337 | ||
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | protease inhibitors | 26071337 | ||
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | inhibitor | 252166693 | ||
| 9153 | SLC28A2 | EXTERNAL SIDE OF PLASMA MEMBRANE, TRANSPORTER, DRUGGABLE GENOME | boceprevir | BOCEPREVIR | 25836019 |
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