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Gene: SNX13 |
Gene summary for SNX13 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SNX13 | Gene ID | 23161 |
| Gene name | sorting nexin 13 | |
| Gene Alias | RGS-PX1 | |
| Cytomap | 7p21.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | A0A024R9Z9 |
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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 |
| 23161 | SNX13 | HTA11_3410_2000001011 | Human | Colorectum | AD | 9.65e-18 | -6.47e-01 | 0.0155 |
| 23161 | SNX13 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.04e-08 | -6.70e-01 | -0.1207 |
| 23161 | SNX13 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.28e-06 | -4.39e-01 | -0.1464 |
| 23161 | SNX13 | HTA11_866_2000001011 | Human | Colorectum | AD | 5.58e-13 | -5.28e-01 | -0.1001 |
| 23161 | SNX13 | HTA11_1391_2000001011 | Human | Colorectum | AD | 7.16e-05 | -4.59e-01 | -0.059 |
| 23161 | SNX13 | HTA11_7862_2000001011 | Human | Colorectum | AD | 2.98e-02 | -5.84e-01 | -0.0179 |
| 23161 | SNX13 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.75e-11 | -5.73e-01 | 0.096 |
| 23161 | SNX13 | HTA11_8622_2000001021 | Human | Colorectum | SER | 8.71e-03 | -6.50e-01 | 0.0528 |
| 23161 | SNX13 | HTA11_10711_2000001011 | Human | Colorectum | AD | 4.19e-07 | -6.00e-01 | 0.0338 |
| 23161 | SNX13 | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.64e-16 | -5.93e-01 | 0.0674 |
| 23161 | SNX13 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 8.69e-11 | -5.08e-01 | 0.294 |
| 23161 | SNX13 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.06e-06 | -4.79e-01 | 0.3859 |
| 23161 | SNX13 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 3.08e-03 | -5.74e-01 | 0.2585 |
| 23161 | SNX13 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.00e-14 | -5.43e-01 | 0.3005 |
| 23161 | SNX13 | A001-C-207 | Human | Colorectum | FAP | 1.33e-02 | -2.08e-01 | 0.1278 |
| 23161 | SNX13 | A015-C-203 | Human | Colorectum | FAP | 3.69e-27 | -3.81e-01 | -0.1294 |
| 23161 | SNX13 | A015-C-204 | Human | Colorectum | FAP | 1.83e-03 | -1.86e-01 | -0.0228 |
| 23161 | SNX13 | A014-C-040 | Human | Colorectum | FAP | 1.38e-03 | -4.30e-01 | -0.1184 |
| 23161 | SNX13 | A002-C-201 | Human | Colorectum | FAP | 5.15e-15 | -3.67e-01 | 0.0324 |
| 23161 | SNX13 | A002-C-203 | Human | Colorectum | FAP | 7.04e-03 | -2.26e-02 | 0.2786 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
| GO:0043547 | Colorectum | AD | positive regulation of GTPase activity | 75/3918 | 255/18723 | 7.95e-04 | 7.91e-03 | 75 |
| GO:00430871 | Colorectum | SER | regulation of GTPase activity | 77/2897 | 348/18723 | 5.90e-04 | 8.07e-03 | 77 |
| GO:00430872 | Colorectum | MSS | regulation of GTPase activity | 101/3467 | 348/18723 | 1.00e-06 | 3.46e-05 | 101 |
| GO:00435471 | Colorectum | MSS | positive regulation of GTPase activity | 68/3467 | 255/18723 | 7.97e-04 | 8.38e-03 | 68 |
| GO:00430873 | Colorectum | FAP | regulation of GTPase activity | 85/2622 | 348/18723 | 1.20e-07 | 7.68e-06 | 85 |
| GO:00435472 | Colorectum | FAP | positive regulation of GTPase activity | 61/2622 | 255/18723 | 1.39e-05 | 3.73e-04 | 61 |
| GO:00430874 | Colorectum | CRC | regulation of GTPase activity | 69/2078 | 348/18723 | 1.11e-06 | 6.69e-05 | 69 |
| GO:00435473 | Colorectum | CRC | positive regulation of GTPase activity | 49/2078 | 255/18723 | 8.67e-05 | 1.77e-03 | 49 |
| GO:004308715 | Esophagus | ESCC | regulation of GTPase activity | 183/8552 | 348/18723 | 5.34e-03 | 2.00e-02 | 183 |
| GO:00430875 | Liver | NAFLD | regulation of GTPase activity | 62/1882 | 348/18723 | 5.65e-06 | 2.03e-04 | 62 |
| GO:00435474 | Liver | NAFLD | positive regulation of GTPase activity | 45/1882 | 255/18723 | 1.30e-04 | 2.47e-03 | 45 |
| GO:00430876 | Lung | IAC | regulation of GTPase activity | 67/2061 | 348/18723 | 3.43e-06 | 1.44e-04 | 67 |
| GO:00435475 | Lung | IAC | positive regulation of GTPase activity | 48/2061 | 255/18723 | 1.40e-04 | 2.60e-03 | 48 |
| GO:004308711 | Lung | AIS | regulation of GTPase activity | 65/1849 | 348/18723 | 3.35e-07 | 2.83e-05 | 65 |
| GO:004354711 | Lung | AIS | positive regulation of GTPase activity | 44/1849 | 255/18723 | 1.74e-04 | 3.64e-03 | 44 |
| GO:004308710 | Oral cavity | OSCC | regulation of GTPase activity | 165/7305 | 348/18723 | 7.94e-04 | 4.27e-03 | 165 |
| GO:004308714 | Oral cavity | EOLP | regulation of GTPase activity | 66/2218 | 348/18723 | 6.92e-05 | 8.55e-04 | 66 |
| GO:00435479 | Oral cavity | EOLP | positive regulation of GTPase activity | 47/2218 | 255/18723 | 1.34e-03 | 9.33e-03 | 47 |
| GO:004308722 | Oral cavity | NEOLP | regulation of GTPase activity | 54/2005 | 348/18723 | 3.36e-03 | 2.00e-02 | 54 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| SNX13 | SNV | Missense_Mutation | novel | c.1963N>C | p.Ala655Pro | p.A655P | Q9Y5W8 | protein_coding | tolerated(0.12) | benign(0.054) | TCGA-A2-A04Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| SNX13 | SNV | Missense_Mutation | novel | c.740N>A | p.Arg247Gln | p.R247Q | Q9Y5W8 | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-A2-A0SY-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | arimidex | SD |
| SNX13 | SNV | Missense_Mutation | c.548N>T | p.Asp183Val | p.D183V | Q9Y5W8 | protein_coding | tolerated(0.11) | benign(0.007) | TCGA-AO-A0J6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| SNX13 | SNV | Missense_Mutation | c.1471N>C | p.Glu491Gln | p.E491Q | Q9Y5W8 | protein_coding | tolerated(0.39) | benign(0.019) | TCGA-B6-A0WZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| SNX13 | SNV | Missense_Mutation | c.1585N>C | p.Asp529His | p.D529H | Q9Y5W8 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SNX13 | SNV | Missense_Mutation | novel | c.1330G>A | p.Gly444Arg | p.G444R | Q9Y5W8 | protein_coding | tolerated(0.09) | possibly_damaging(0.653) | TCGA-EW-A2FR-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | epirubicin | SD |
| SNX13 | SNV | Missense_Mutation | novel | c.1622N>A | p.Gly541Glu | p.G541E | Q9Y5W8 | protein_coding | tolerated(0.08) | benign(0.022) | TCGA-XX-A89A-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SNX13 | SNV | Missense_Mutation | novel | c.1907G>A | p.Arg636Lys | p.R636K | Q9Y5W8 | protein_coding | tolerated(0.36) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SNX13 | SNV | Missense_Mutation | c.2515N>A | p.Asp839Asn | p.D839N | Q9Y5W8 | protein_coding | tolerated(0.34) | benign(0.013) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| SNX13 | SNV | Missense_Mutation | c.1423N>A | p.Glu475Lys | p.E475K | Q9Y5W8 | protein_coding | tolerated(0.16) | possibly_damaging(0.574) | TCGA-MU-A51Y-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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