|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for VAPB |
Top |
Phenotypic Information for VAPB(metabolism pathway, cancer, disease, phenome) |
![]() | |
Cancer | CGAP: VAPB |
Familial Cancer Database: VAPB |
* 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/ |
![]() | |
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
![]() | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: VAPB |
MedGen: VAPB (Human Medical Genetics with Condition) | |
ClinVar: VAPB | |
Phenotype | MGI: VAPB (International Mouse Phenotyping Consortium) |
PhenomicDB: VAPB |
Mutations for VAPB |
* 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. |
![]() |
- 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 |
ovary | VAPB | chr20 | 56979777 | 56979797 | VAPB | chr20 | 56981528 | 56981548 |
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) |
![]() |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows VAPB 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 |
XX000009 | VAPB | 1 | 67 | 20 | 56964507 | 56964573 | IKZF3 | 66 | 166 | 17 | 37933922 | 37934022 | |
AW993740 | VAPB | 1 | 337 | 20 | 56979196 | 56979533 | DMD | 331 | 582 | X | 31213612 | 31213863 | |
AI093537 | DAXX | 24 | 246 | 6 | 4518583 | 4519208 | VAPB | 242 | 420 | 20 | 57020285 | 57020463 | |
BF872158 | VAPB | 1 | 136 | 20 | 57010521 | 57010657 | VAPB | 132 | 394 | 20 | 56999371 | 56999633 |
![]() |
Top |
![]() |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 10 | 1 |   | 1 |   |   | 2 |   |   |   | 1 |   |   | 2 |   |   |   | |||
GAIN (# sample) | 10 | 1 |   | 1 |   |   | 2 |   |   |   | 1 |   |   | 2 |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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) |
Top |
![]() |
|
![]() |
Top |
![]() |
Stat. for Non-Synonymous SNVs (# total SNVs=19) | (# total SNVs=4) |
![]() | ![]() |
(# total SNVs=0) | (# total SNVs=0) |
Top |
![]() |
* 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 |
chr20:57016059-57016059 | p.E165K | 4 |
chr20:57009663-57009663 | p.L73L | 1 |
chr20:57016116-57016116 | p.R184W | 1 |
chr20:56993269-56993269 | p.P21S | 1 |
chr20:57009708-57009708 | p.F88V | 1 |
chr20:57016123-57016123 | p.E186G | 1 |
chr20:56993271-56993271 | p.P21P | 1 |
chr20:57009745-57009745 | p.S100* | 1 |
chr20:57019206-57019206 | p.K216M | 1 |
chr20:56993278-56993278 | p.D24N | 1 |
Top |
![]() |
|
![]() |
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 |   |   |   | 5 |   |   | 1 |   | 1 |   |   | 2 | 1 |   |   |   | 3 | 1 |   | 5 |
# mutation |   |   |   | 5 |   |   | 1 |   | 1 |   |   | 2 | 1 |   |   |   | 3 | 1 |   | 5 |
nonsynonymous SNV |   |   |   | 3 |   |   |   |   | 1 |   |   | 1 | 1 |   |   |   | 2 |   |   | 5 |
synonymous SNV |   |   |   | 2 |   |   | 1 |   |   |   |   | 1 |   |   |   |   | 1 | 1 |   |   |
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]) |
Top |
![]() |
* 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 |
chr20:57015989 | p.E186G | 1 |
chr20:56993269 | p.P21S,VAPB | 1 |
chr20:57015992 | p.I233I | 1 |
chr20:56993271 | p.P21P,VAPB | 1 |
chr20:57016022 | p.V234I | 1 |
chr20:56993278 | p.D24N,VAPB | 1 |
chr20:57016033 | p.V236L | 1 |
chr20:56993321 | p.R38Q,VAPB | 1 |
chr20:57016116 | p.R50R,VAPB | 1 |
chr20:56993358 | p.R51G,VAPB | 1 |
![]() |
![]() |
* 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] |
Top |
Gene Expression for VAPB |
![]() |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
![]() |
![]() |
* 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)) |
![]() |
Top |
![]() |
* This plots show the correlation between CNV and gene expression. |
![]() | |
![]() |
Top |
Gene-Gene Network Information |
![]() |
* 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 |
![]() | |
ARFGEF2,GID8,FAM217B,RTFDC1,CSE1L,CSTF1,DNAJC5, EEF1A2,LSM14B,NPEPL1,OSBPL2,PPP1R3D,PSMA7,RAB22A, RAE1,SLMO2,SS18L1,STX16,TAF4,NELFCD,VAPB | ALDH5A1,CMBL,CSNK2A3,CUL4A,DCAF5,DCAF8,HBS1L, HECTD1,HSPA9,KIAA0368,L2HGDH,LOC729082,NDUFS1,NRD1, PRKAR2A,SOX6,STAU2,UQCC1,USO1,VAPB,ZFYVE9 |
![]() | |
GID8,AAR2,RTFDC1,CSE1L,CSTF1,DDX27,DPM1, DSN1,TTI1,MOCS3,RAE1,RPRD1B,SLMO2,SPATA2, STAU1,TAF4,NELFCD,TP53RK,UBE2V1,VAPB,YTHDF1 | ARL8B,ASB8,ATL3,ATP5J,ATP6V1E1,MINOS1,CAMTA1, COX6C,DNAJA2,EFR3A,RMDN1,KPNA4,PSMC1,RAB18, RAB6A,RHOA,SBDS,SEC23A,UHRF1BP1L,VAPB,YWHAQ |
![]() |
* 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 |
Top |
![]() |
Top |
Pharmacological Information for VAPB |
There's no related Drug. |
Top |
Cross referenced IDs for VAPB |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |