|
|||||
|
 | |
| |
| |
| |
| |
| |
|
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 |
Top |
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. |
Top |
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:00988762 | Colorectum | MSS | vesicle-mediated transport to the plasma membrane | 54/3467 | 136/18723 | 6.20e-09 | 3.95e-07 | 54 |
| GO:00161972 | Colorectum | MSS | endosomal transport | 79/3467 | 230/18723 | 7.04e-09 | 4.39e-07 | 79 |
| GO:00301002 | Colorectum | MSS | regulation of endocytosis | 63/3467 | 211/18723 | 4.05e-05 | 7.66e-04 | 63 |
| GO:00068981 | Colorectum | MSS | receptor-mediated endocytosis | 69/3467 | 244/18723 | 1.18e-04 | 1.82e-03 | 69 |
| GO:00060662 | Colorectum | MSS | alcohol metabolic process | 92/3467 | 353/18723 | 2.57e-04 | 3.46e-03 | 92 |
| GO:00324561 | Colorectum | MSS | endocytic recycling | 26/3467 | 73/18723 | 4.05e-04 | 4.99e-03 | 26 |
| GO:00442822 | Colorectum | MSS | small molecule catabolic process | 94/3467 | 376/18723 | 9.85e-04 | 9.86e-03 | 94 |
| GO:0001655 | Colorectum | MSS | urogenital system development | 81/3467 | 338/18723 | 6.88e-03 | 4.43e-02 | 81 |
| GO:00160422 | Colorectum | MSS | lipid catabolic process | 77/3467 | 320/18723 | 7.43e-03 | 4.71e-02 | 77 |
| GO:190136117 | Esophagus | HGIN | organic cyclic compound catabolic process | 106/2587 | 495/18723 | 1.94e-06 | 7.13e-05 | 106 |
| GO:001619710 | Esophagus | HGIN | endosomal transport | 57/2587 | 230/18723 | 5.74e-06 | 1.81e-04 | 57 |
| GO:009887610 | Esophagus | HGIN | vesicle-mediated transport to the plasma membrane | 36/2587 | 136/18723 | 6.76e-05 | 1.55e-03 | 36 |
| GO:001619715 | Esophagus | ESCC | endosomal transport | 168/8552 | 230/18723 | 2.28e-17 | 1.93e-15 | 168 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:009887615 | Esophagus | ESCC | vesicle-mediated transport to the plasma membrane | 99/8552 | 136/18723 | 1.13e-10 | 3.39e-09 | 99 |
| GO:003010018 | Esophagus | ESCC | regulation of endocytosis | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:00060668 | Esophagus | ESCC | alcohol metabolic process | 202/8552 | 353/18723 | 7.32e-06 | 7.26e-05 | 202 |
| GO:00324565 | Esophagus | ESCC | endocytic recycling | 51/8552 | 73/18723 | 2.47e-05 | 2.10e-04 | 51 |
| GO:000689818 | Esophagus | ESCC | receptor-mediated endocytosis | 142/8552 | 244/18723 | 5.22e-05 | 4.05e-04 | 142 |
| GO:19026524 | Esophagus | ESCC | secondary alcohol metabolic process | 87/8552 | 147/18723 | 6.58e-04 | 3.50e-03 | 87 |
| 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 |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |