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| TissGeneSummary for VCX3A |
 Gene summary |
| Basic gene information | Gene symbol | VCX3A |
| Gene name | variable charge, X-linked 3A | |
| Synonyms | VCX-8r|VCX-A|VCX3|VCX8R|VCXA | |
| Cytomap | UCSC genome browser: Xp22 | |
| Type of gene | protein-coding | |
| RefGenes | NM_016379.3, | |
| Description | variable charge X-linked protein 3variable charge protein on X with eight repeatsvariably charged X-Avariably charged protein X-A | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 300533 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000169059 | ||
| HPRD : 18280 | ||
| Vega : OTTHUMG00000021097 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_VCX3A | |
| BioGPS: 51481 | ||
| Pathway | NCI Pathway Interaction Database: VCX3A | |
| KEGG: VCX3A | ||
| REACTOME: VCX3A | ||
| Pathway Commons: VCX3A | ||
| Context | iHOP: VCX3A | |
| ligand binding site mutation search in PubMed: VCX3A | ||
| UCL Cancer Institute: VCX3A | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | HPA,GTEx | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Testis | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
| Reference showing the relevant tissue of VCX3A | ||
| Description by TissGene annotations | Cancer gene | |
| * Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO term | PubMed ID |
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| TissGeneExp for VCX3A |
| Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
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| Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
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| Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
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| Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
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| - Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
| Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
| LUSC | -0.142489611 | -2.104370003 | 1.961880392 | 1.06E-11 | 4.40E-11 |
| KICH | -0.171204278 | -1.676224278 | 1.50502 | 1.22E-05 | 3.81E-05 |
| LIHC | -0.359912278 | -2.007840278 | 1.647928 | 4.69E-06 | 2.15E-05 |
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| TissGene-miRNA for VCX3A |
| Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
| Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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| TissGeneMut for VCX3A |
| TissGeneSNV for VCX3A |
| nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
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| Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.L154P | COAD | 1 |
| p.E171Q | BRCA | 1 |
| p.E181K | SKCM | 1 |
| p.E167* | LUSC | 1 |
| p.L164P | COAD | 1 |
| p.E179K | STAD | 1 |
| p.S175R | LGG | 1 |
| p.E172D | STAD | 1 |
| p.V140M | UCEC | 1 |
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| TissGeneCNV for VCX3A |
| Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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| TissGeneFusions for VCX3A |
| Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
| Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
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| TissGeneNet for VCX3A |
| Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
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| TissGeneProg for VCX3A |
| Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
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| Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| TissGeneClin for VCX3A |
| TissGeneDrug for VCX3A |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| TissGeneDisease for VCX3A |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0025362 | Mental Retardation | 7 | BeFree |
| umls:C0079588 | Ichthyosis, X-Linked | 4 | BeFree |
| umls:C2720163 | Placental Steroid Sulfatase Deficiency | 4 | BeFree |
| umls:C0006009 | Borderline mental retardation (I.Q. 70-85) | 1 | BeFree |
| umls:C1136249 | Mental Retardation, X-Linked | 1 | BeFree |
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