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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for VAC14 |
Basic gene info. | Gene symbol | VAC14 |
Gene name | Vac14 homolog (S. cerevisiae) | |
Synonyms | ArPIKfyve|TAX1BP2|TRX | |
Cytomap | UCSC genome browser: 16q22.1 | |
Genomic location | chr16 :70721341-70835061 | |
Type of gene | protein-coding | |
RefGenes | NM_018052.3, | |
Ensembl id | ENSG00000103043 | |
Description | Tax1 (human T-cell leukemia virus type I) binding protein 1Tax1 (human T-cell leukemia virus type I) binding protein 2protein VAC14 homologtax1-binding protein 2 | |
Modification date | 20141207 | |
dbXrefs | MIM : 604632 | |
HGNC : HGNC | ||
Ensembl : ENSG00000103043 | ||
HPRD : 07660 | ||
Vega : OTTHUMG00000137583 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_VAC14 | |
BioGPS: 55697 | ||
Gene Expression Atlas: ENSG00000103043 | ||
The Human Protein Atlas: ENSG00000103043 | ||
Pathway | NCI Pathway Interaction Database: VAC14 | |
KEGG: VAC14 | ||
REACTOME: VAC14 | ||
ConsensusPathDB | ||
Pathway Commons: VAC14 | ||
Metabolism | MetaCyc: VAC14 | |
HUMANCyc: VAC14 | ||
Regulation | Ensembl's Regulation: ENSG00000103043 | |
miRBase: chr16 :70,721,341-70,835,061 | ||
TargetScan: NM_018052 | ||
cisRED: ENSG00000103043 | ||
Context | iHOP: VAC14 | |
cancer metabolism search in PubMed: VAC14 | ||
UCL Cancer Institute: VAC14 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for VAC14(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: VAC14 |
Familial Cancer Database: VAC14 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: VAC14 |
MedGen: VAC14 (Human Medical Genetics with Condition) | |
ClinVar: VAC14 | |
Phenotype | MGI: VAC14 (International Mouse Phenotyping Consortium) |
PhenomicDB: VAC14 |
Mutations for VAC14 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | VAC14 | chr16 | 70743975 | 70743995 | IL34 | chr16 | 70687966 | 70687986 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows VAC14 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BF756717 | VAC14 | 4 | 208 | 16 | 70765362 | 70778361 | CENPT | 206 | 280 | 16 | 67866188 | 67866401 | |
BP265165 | UBE2G1 | 1 | 426 | 17 | 4174845 | 4175271 | VAC14 | 423 | 577 | 16 | 70817345 | 70818057 | |
CV310892 | VAC14 | 16 | 259 | 16 | 70826837 | 70827080 | VAC14 | 258 | 407 | 16 | 70827610 | 70827759 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 4 |   |   | 1 |   |   |   |   | 1 |   |   |   |   | 1 | 1 |   |   | |||
GAIN (# sample) | 2 |   |   | 1 |   |   |   |   | 1 |   |   |   |   |   | 1 |   |   | |||
LOSS (# sample) | 2 |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=49) | (# total SNVs=16) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr16:70729468-70729468 | p.I672F | 7 |
chr16:70796852-70796852 | p.I413F | 2 |
chr16:70796894-70796894 | p.G399W | 2 |
chr16:70796903-70796903 | p.H396Y | 2 |
chr16:70817355-70817355 | p.R233C | 2 |
chr16:70732623-70732623 | p.M585V | 2 |
chr16:70815792-70815792 | p.A309V | 2 |
chr16:70765531-70765531 | p.? | 1 |
chr16:70818069-70818069 | p.R181* | 1 |
chr16:70726795-70726795 | p.P705P | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 2 | 3 |   | 5 |   |   |   |   | 3 |   |   | 7 | 2 | 1 |   | 1 | 6 | 3 | 1 | 8 |
# mutation | 2 | 3 |   | 5 |   |   |   |   | 3 |   |   | 8 | 2 | 1 |   | 1 | 7 | 4 | 1 | 8 |
nonsynonymous SNV | 2 | 3 |   | 3 |   |   |   |   | 3 |   |   | 6 | 2 | 1 |   |   | 4 | 1 | 1 | 4 |
synonymous SNV |   |   |   | 2 |   |   |   |   |   |   |   | 2 |   |   |   | 1 | 3 | 3 |   | 4 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr16:70815792 | p.G399R | 2 |
chr16:70796894 | p.H396Y | 2 |
chr16:70796903 | p.A309V | 2 |
chr16:70817441 | p.S472S | 1 |
chr16:70765459 | p.S204L | 1 |
chr16:70820260 | p.I469I | 1 |
chr16:70796918 | p.S175R | 1 |
chr16:70818087 | p.Q759K | 1 |
chr16:70765486 | p.T411T | 1 |
chr16:70834740 | p.E167Q | 1 |
Other DBs for Point Mutations |
Copy Number for VAC14 in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for VAC14 |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
ACD,CHMP1A,COG4,EMC8,CTU2,DDX19A,DDX19B, DDX28,DHX38,DUS2,E2F4,EDC4,KARS,NUP93, NUTF2,PSMD7,THAP11,VAC14,VPS4A,ZC3H18,ZNRF1 | AMDHD2,B4GALT7,VPS9D1,CCDC22,CHMP1A,CLCN7,DGKZ, AP5Z1,MBD3,MED15,MPND,NCLN,PNPLA6,PQLC2, RABGGTA,RANBP3,RPS6KB2,PPP6R1,SCYL1,VAC14,VPS18 |
C16orf70,CHMP1A,CLCN7,COG4,CORO7,DDX19A,DHX38, E2F4,EDC4,MTHFSD,NPRL3,NUP93,PSKH1,SETD1A, SLC7A6OS,SPNS1,TANGO6,VAC14,VPS4A,XPO6,ZC3H18 | ANAPC2,CLCN7,CTBP1,DDX54,DHX38,DOHH,FZR1, INTS1,MBD3,NF2,PHRF1,POLRMT,RNF40,SART1, SBF1,SCAF1,STK11IP,TBL3,TUBGCP2,VAC14,WDR81 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for VAC14 |
There's no related Drug. |
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Cross referenced IDs for VAC14 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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