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Gene: VCX3A |
Gene summary for VCX3A |
Gene summary. |
Gene information | Species | Human | Gene symbol | VCX3A | Gene ID | 51481 |
Gene name | variable charge X-linked 3A | |
Gene Alias | VCX-8r | |
Cytomap | Xp22.31 | |
Gene Type | protein-coding | GO ID | GO:0007275 | UniProtAcc | Q9NNX9 |
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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 |
51481 | VCX3A | HCC2 | Human | Liver | HCC | 5.11e-07 | 2.06e+00 | 0.5341 |
51481 | VCX3A | S014 | Human | Liver | HCC | 1.10e-15 | 8.04e-01 | 0.2254 |
51481 | VCX3A | S015 | Human | Liver | HCC | 1.71e-04 | 2.98e-01 | 0.2375 |
51481 | VCX3A | S016 | Human | Liver | HCC | 2.63e-03 | 2.97e-01 | 0.2243 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Liver | HCC: Hepatocellular carcinoma | |
NAFLD: Non-alcoholic fatty liver disease |
∗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 |
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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 |
VCX3A | SNV | Missense_Mutation | novel | c.220N>T | p.Pro74Ser | p.P74S | Q9NNX9 | protein_coding | tolerated_low_confidence(0.18) | benign(0.188) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VCX3A | SNV | Missense_Mutation | rs770386321 | c.304N>A | p.Asp102Asn | p.D102N | Q9NNX9 | protein_coding | deleterious(0.01) | benign(0.274) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
VCX3A | SNV | Missense_Mutation | novel | c.351N>T | p.Glu117Asp | p.E117D | Q9NNX9 | protein_coding | tolerated(0.17) | possibly_damaging(0.583) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VCX3A | SNV | Missense_Mutation | rs749763251 | c.232N>A | p.Asp78Asn | p.D78N | Q9NNX9 | protein_coding | tolerated(0.16) | benign(0.031) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
VCX3A | SNV | Missense_Mutation | novel | c.259C>T | p.His87Tyr | p.H87Y | Q9NNX9 | protein_coding | tolerated(1) | benign(0.087) | TCGA-AX-A3G8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VCX3A | SNV | Missense_Mutation | rs200714581 | c.415N>C | p.Glu139Gln | p.E139Q | Q9NNX9 | protein_coding | tolerated(0.61) | benign(0.15) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
VCX3A | SNV | Missense_Mutation | novel | c.158N>C | p.Lys53Thr | p.K53T | Q9NNX9 | protein_coding | tolerated_low_confidence(0.05) | possibly_damaging(0.598) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
VCX3A | SNV | Missense_Mutation | novel | c.116N>T | p.Ala39Val | p.A39V | Q9NNX9 | protein_coding | tolerated_low_confidence(0.08) | benign(0.266) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
VCX3A | SNV | Missense_Mutation | novel | c.143N>A | p.Gly48Glu | p.G48E | Q9NNX9 | protein_coding | deleterious_low_confidence(0.02) | probably_damaging(0.912) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VCX3A | SNV | Missense_Mutation | novel | c.130G>T | p.Ala44Ser | p.A44S | Q9NNX9 | protein_coding | deleterious_low_confidence(0.04) | possibly_damaging(0.65) | TCGA-EO-A22U-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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