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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 | c.346T>C | p.Ser116Pro | p.S116P | Q92543 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BS-A0TC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SNX19 | SNV | Missense_Mutation | c.2297N>A | p.Ser766Tyr | p.S766Y | Q92543 | protein_coding | deleterious(0) | possibly_damaging(0.643) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SNX19 | SNV | Missense_Mutation | novel | c.1124N>A | p.Ser375Tyr | p.S375Y | Q92543 | protein_coding | deleterious(0) | possibly_damaging(0.896) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SNX19 | SNV | Missense_Mutation | c.2072N>T | p.Ala691Val | p.A691V | Q92543 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BS-A0UL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SNX19 | SNV | Missense_Mutation | rs758976076 | c.2776N>A | p.Leu926Ile | p.L926I | Q92543 | protein_coding | deleterious(0.01) | probably_damaging(0.973) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
SNX19 | SNV | Missense_Mutation | novel | c.2266N>C | p.Ser756Pro | p.S756P | Q92543 | protein_coding | tolerated(0.23) | possibly_damaging(0.791) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
SNX19 | SNV | Missense_Mutation | c.2828A>G | p.Gln943Arg | p.Q943R | Q92543 | protein_coding | deleterious(0.01) | probably_damaging(0.955) | TCGA-D1-A174-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SNX19 | SNV | Missense_Mutation | rs140963839 | c.1987N>T | p.Arg663Cys | p.R663C | Q92543 | protein_coding | deleterious(0.03) | possibly_damaging(0.502) | TCGA-D1-A17Q-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SNX19 | SNV | Missense_Mutation | novel | c.2941N>G | p.Thr981Ala | p.T981A | Q92543 | protein_coding | tolerated(0.34) | benign(0) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
SNX19 | SNV | Missense_Mutation | rs537471912 | c.2545N>T | p.Arg849Cys | p.R849C | Q92543 | protein_coding | deleterious(0) | probably_damaging(0.911) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | 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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