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Gene: SNX17 |
Gene summary for SNX17 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SNX17 | Gene ID | 9784 |
| Gene name | sorting nexin 17 | |
| Gene Alias | SNX17 | |
| Cytomap | 2p23.3 | |
| Gene Type | protein-coding | GO ID | GO:0001568 | UniProtAcc | B4DTB8 |
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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 |
| 9784 | SNX17 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.73e-06 | 3.40e-01 | -0.1808 |
| 9784 | SNX17 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.87e-06 | 3.27e-01 | -0.0811 |
| 9784 | SNX17 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.70e-05 | 2.94e-01 | -0.1088 |
| 9784 | SNX17 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.86e-11 | 3.28e-01 | -0.1954 |
| 9784 | SNX17 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.33e-07 | 3.55e-01 | -0.1207 |
| 9784 | SNX17 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.26e-02 | 1.94e-01 | -0.1526 |
| 9784 | SNX17 | HTA11_696_2000001011 | Human | Colorectum | AD | 6.53e-12 | 2.63e-01 | -0.1464 |
| 9784 | SNX17 | HTA11_866_2000001011 | Human | Colorectum | AD | 9.62e-04 | 1.73e-01 | -0.1001 |
| 9784 | SNX17 | HTA11_1391_2000001011 | Human | Colorectum | AD | 8.66e-12 | 4.02e-01 | -0.059 |
| 9784 | SNX17 | HTA11_5212_2000001011 | Human | Colorectum | AD | 5.00e-04 | 3.18e-01 | -0.2061 |
| 9784 | SNX17 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.86e-13 | 3.61e-01 | 0.096 |
| 9784 | SNX17 | HTA11_8622_2000001021 | Human | Colorectum | SER | 3.76e-02 | 2.63e-01 | 0.0528 |
| 9784 | SNX17 | HTA11_7663_2000001011 | Human | Colorectum | SER | 2.53e-02 | 3.35e-01 | 0.0131 |
| 9784 | SNX17 | HTA11_10623_2000001011 | Human | Colorectum | AD | 1.76e-04 | 3.29e-01 | -0.0177 |
| 9784 | SNX17 | HTA11_10711_2000001011 | Human | Colorectum | AD | 4.13e-02 | 2.34e-01 | 0.0338 |
| 9784 | SNX17 | HTA11_7696_3000711011 | Human | Colorectum | AD | 9.74e-08 | 2.10e-01 | 0.0674 |
| 9784 | SNX17 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.67e-09 | 3.43e-01 | 0.294 |
| 9784 | SNX17 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.01e-11 | 5.31e-01 | 0.281 |
| 9784 | SNX17 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.01e-11 | 3.17e-01 | 0.3859 |
| 9784 | SNX17 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.10e-07 | 4.47e-01 | 0.2585 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| 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:0016197 | Colorectum | AD | endosomal transport | 90/3918 | 230/18723 | 1.88e-10 | 1.73e-08 | 90 |
| GO:0098876 | Colorectum | AD | vesicle-mediated transport to the plasma membrane | 57/3918 | 136/18723 | 2.30e-08 | 1.27e-06 | 57 |
| GO:1901361 | Colorectum | AD | organic cyclic compound catabolic process | 153/3918 | 495/18723 | 8.23e-08 | 4.18e-06 | 153 |
| GO:0044282 | Colorectum | AD | small molecule catabolic process | 118/3918 | 376/18723 | 1.05e-06 | 3.55e-05 | 118 |
| GO:0006066 | Colorectum | AD | alcohol metabolic process | 106/3918 | 353/18723 | 3.02e-05 | 5.57e-04 | 106 |
| GO:0016042 | Colorectum | AD | lipid catabolic process | 97/3918 | 320/18723 | 4.31e-05 | 7.56e-04 | 97 |
| GO:0006898 | Colorectum | AD | receptor-mediated endocytosis | 76/3918 | 244/18723 | 1.07e-04 | 1.59e-03 | 76 |
| GO:0030100 | Colorectum | AD | regulation of endocytosis | 67/3918 | 211/18723 | 1.42e-04 | 2.01e-03 | 67 |
| GO:0032456 | Colorectum | AD | endocytic recycling | 28/3918 | 73/18723 | 4.87e-04 | 5.30e-03 | 28 |
| GO:0046164 | Colorectum | AD | alcohol catabolic process | 20/3918 | 55/18723 | 6.03e-03 | 3.78e-02 | 20 |
| GO:0008202 | Colorectum | AD | steroid metabolic process | 85/3918 | 319/18723 | 8.07e-03 | 4.75e-02 | 85 |
| GO:00161971 | Colorectum | SER | endosomal transport | 61/2897 | 230/18723 | 1.03e-05 | 3.35e-04 | 61 |
| GO:00160421 | Colorectum | SER | lipid catabolic process | 77/2897 | 320/18723 | 3.52e-05 | 9.18e-04 | 77 |
| GO:00442821 | Colorectum | SER | small molecule catabolic process | 87/2897 | 376/18723 | 5.31e-05 | 1.27e-03 | 87 |
| GO:00988761 | Colorectum | SER | vesicle-mediated transport to the plasma membrane | 37/2897 | 136/18723 | 3.08e-04 | 5.00e-03 | 37 |
| GO:00060661 | Colorectum | SER | alcohol metabolic process | 79/2897 | 353/18723 | 3.50e-04 | 5.50e-03 | 79 |
| GO:19013611 | Colorectum | SER | organic cyclic compound catabolic process | 104/2897 | 495/18723 | 5.46e-04 | 7.63e-03 | 104 |
| GO:00461641 | Colorectum | SER | alcohol catabolic process | 17/2897 | 55/18723 | 3.00e-03 | 2.65e-02 | 17 |
| GO:00301001 | Colorectum | SER | regulation of endocytosis | 48/2897 | 211/18723 | 3.29e-03 | 2.82e-02 | 48 |
| GO:19013612 | Colorectum | MSS | organic cyclic compound catabolic process | 148/3467 | 495/18723 | 3.47e-10 | 3.18e-08 | 148 |
| 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 |
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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 |
| SNX17 | SNV | Missense_Mutation | rs756756686 | c.827N>T | p.Ala276Val | p.A276V | Q15036 | protein_coding | deleterious(0) | benign(0.043) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| SNX17 | SNV | Missense_Mutation | rs747689756 | c.708N>T | p.Trp236Cys | p.W236C | Q15036 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| SNX17 | SNV | Missense_Mutation | c.1034N>A | p.Arg345His | p.R345H | Q15036 | protein_coding | tolerated(0.1) | benign(0.006) | TCGA-AQ-A1H3-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| SNX17 | SNV | Missense_Mutation | novel | c.954N>A | p.Met318Ile | p.M318I | Q15036 | protein_coding | tolerated(0.24) | benign(0.134) | TCGA-B6-A3ZX-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
| SNX17 | SNV | Missense_Mutation | c.1054N>A | p.Tyr352Asn | p.Y352N | Q15036 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E2-A1LL-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | docetaxel | PD | |
| SNX17 | SNV | Missense_Mutation | novel | c.968T>G | p.Val323Gly | p.V323G | Q15036 | protein_coding | deleterious(0) | possibly_damaging(0.536) | TCGA-OL-A6VO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| SNX17 | insertion | In_Frame_Ins | novel | c.281_282insTGGTTTTCTGTCCAGTCTTACTGCTCTAGTAGCCTTTAC | p.Ser94_Ser95insGlyPheLeuSerSerLeuThrAlaLeuValAlaPheThr | p.S94_S95insGFLSSLTALVAFT | Q15036 | protein_coding | TCGA-A2-A0D0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| SNX17 | insertion | Frame_Shift_Ins | novel | c.1390_1391insACCTGAT | p.Gly464AspfsTer7 | p.G464Dfs*7 | Q15036 | protein_coding | TCGA-AQ-A04J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| SNX17 | insertion | Frame_Shift_Ins | novel | c.1392_1393insCACCCGGGAGTCTATGGTCAAACTCTCAGTG | p.Ile465HisfsTer14 | p.I465Hfs*14 | Q15036 | protein_coding | TCGA-AQ-A04J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| SNX17 | insertion | Nonsense_Mutation | novel | c.142_143insCCAGATCTTAAACTCTATTTAACTCA | p.Arg48ProfsTer4 | p.R48Pfs*4 | Q15036 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | 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 |
| Page: 1 |
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