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Gene: SNX19 |
Gene summary for SNX19 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SNX19 | Gene ID | 399979 |
| Gene name | sorting nexin 19 | |
| Gene Alias | CHET8 | |
| Cytomap | 11q24.3-q25 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | B7ZAU9 |
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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 |
| 399979 | SNX19 | C04 | Human | Oral cavity | OSCC | 8.34e-15 | 6.01e-01 | 0.2633 |
| 399979 | SNX19 | C21 | Human | Oral cavity | OSCC | 1.22e-03 | 2.18e-01 | 0.2678 |
| 399979 | SNX19 | C30 | Human | Oral cavity | OSCC | 1.13e-18 | 7.23e-01 | 0.3055 |
| 399979 | SNX19 | C51 | Human | Oral cavity | OSCC | 6.39e-03 | 2.01e-01 | 0.2674 |
| 399979 | SNX19 | SYSMH1 | Human | Oral cavity | OSCC | 1.71e-07 | 2.08e-01 | 0.1127 |
| 399979 | SNX19 | SYSMH2 | Human | Oral cavity | OSCC | 1.39e-03 | 1.90e-01 | 0.2326 |
| 399979 | SNX19 | SYSMH3 | Human | Oral cavity | OSCC | 1.30e-07 | 2.21e-01 | 0.2442 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:00160508 | Oral cavity | OSCC | vesicle organization | 189/7305 | 300/18723 | 2.40e-17 | 2.14e-15 | 189 |
| GO:000930610 | Oral cavity | OSCC | protein secretion | 169/7305 | 359/18723 | 1.04e-03 | 5.34e-03 | 169 |
| GO:003559210 | Oral cavity | OSCC | establishment of protein localization to extracellular region | 169/7305 | 360/18723 | 1.21e-03 | 6.08e-03 | 169 |
| GO:00716929 | Oral cavity | OSCC | protein localization to extracellular region | 172/7305 | 368/18723 | 1.40e-03 | 6.79e-03 | 172 |
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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 |
| SNX19 | SNV | Missense_Mutation | rs750218534 | c.1085G>A | p.Arg362Gln | p.R362Q | Q92543 | protein_coding | tolerated(0.41) | benign(0.018) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| SNX19 | SNV | Missense_Mutation | c.2254G>C | p.Gly752Arg | p.G752R | Q92543 | protein_coding | tolerated(0.11) | benign(0.074) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SNX19 | SNV | Missense_Mutation | rs375635584 | c.2084C>G | p.Ser695Cys | p.S695C | Q92543 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AN-A0FS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SNX19 | SNV | Missense_Mutation | rs772538983 | c.1423N>C | p.Thr475Pro | p.T475P | Q92543 | protein_coding | tolerated(0.25) | benign(0) | TCGA-C8-A12X-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SNX19 | SNV | Missense_Mutation | novel | c.1727A>G | p.Tyr576Cys | p.Y576C | Q92543 | protein_coding | deleterious(0.02) | possibly_damaging(0.696) | TCGA-D8-A1X5-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD |
| SNX19 | insertion | Frame_Shift_Ins | novel | c.1829_1830insCACATTTT | p.Lys610AsnfsTer4 | p.K610Nfs*4 | Q92543 | protein_coding | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SNX19 | insertion | In_Frame_Ins | novel | c.1410_1411insTGGGTTTGGAAAGCAGTCATGAAGCAAATGTTCTTGGGGGAGAGA | p.Glu470_Gly471insTrpValTrpLysAlaValMetLysGlnMetPheLeuGlyGluArg | p.E470_G471insWVWKAVMKQMFLGER | Q92543 | protein_coding | TCGA-BH-A0HU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | ||
| SNX19 | SNV | Missense_Mutation | novel | c.1959N>T | p.Gln653His | p.Q653H | Q92543 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SNX19 | SNV | Missense_Mutation | rs774896319 | c.584N>T | p.Ala195Val | p.A195V | Q92543 | protein_coding | tolerated(0.72) | benign(0.011) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SNX19 | SNV | Missense_Mutation | c.2362N>A | p.Glu788Lys | p.E788K | Q92543 | protein_coding | tolerated(0.37) | benign(0.025) | TCGA-DG-A2KH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
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