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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for B3GNT4 |
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Phenotypic Information for B3GNT4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: B3GNT4 |
Familial Cancer Database: B3GNT4 |
* 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_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: B3GNT4 |
MedGen: B3GNT4 (Human Medical Genetics with Condition) | |
ClinVar: B3GNT4 | |
Phenotype | MGI: B3GNT4 (International Mouse Phenotyping Consortium) |
PhenomicDB: B3GNT4 |
Mutations for B3GNT4 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows B3GNT4 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 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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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=29) | (# total SNVs=7) |
(# total SNVs=0) | (# total SNVs=1) |
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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 |
chr12:122691861-122691861 | p.E355K | 3 |
chr12:122690947-122690947 | p.R50M | 2 |
chr12:122691663-122691663 | p.R289W | 2 |
chr12:122691667-122691667 | p.R290H | 2 |
chr12:122691608-122691608 | p.T270T | 2 |
chr12:122691165-122691165 | p.A123T | 1 |
chr12:122691894-122691894 | p.E366K | 1 |
chr12:122691420-122691420 | p.C208R | 1 |
chr12:122691617-122691617 | p.P273P | 1 |
chr12:122691188-122691188 | p.H130H | 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 | 1 | 1 | 1 | 5 |   |   |   |   | 1 |   |   | 1 | 1 | 2 |   | 1 | 5 | 4 |   | 3 |
# mutation | 1 | 1 | 2 | 5 |   |   |   |   | 1 |   |   | 1 | 1 | 2 |   | 1 | 4 | 4 |   | 5 |
nonsynonymous SNV | 1 | 1 |   | 4 |   |   |   |   |   |   |   | 1 | 1 | 2 |   | 1 | 2 | 4 |   | 3 |
synonymous SNV |   |   | 2 | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   | 2 |   |   | 2 |
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 |
chr12:122691861 | p.E355K | 3 |
chr12:122691608 | p.T270T | 2 |
chr12:122691326 | p.P69T | 1 |
chr12:122691811 | p.R289W | 1 |
chr12:122690993 | p.R75Q | 1 |
chr12:122691336 | p.R290C | 1 |
chr12:122691843 | p.A85T | 1 |
chr12:122691003 | p.R290H | 1 |
chr12:122691461 | p.R94C | 1 |
chr12:122691022 | p.A323V | 1 |
Other DBs for Point Mutations |
Copy Number for B3GNT4 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 B3GNT4 |
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 |
AURKB,B3GNT4,CA9,CDC20,EIF3B,ENO1,GJB3, GPI,HMGA1,LY6E,MRPS5,NMB,NUDT1,PFKP, PRDX4,RPUSD3,RRP1,S100A10,TBRG4,TUBA1C,WDR4 | ANO9,ATP1A1,B3GNT4,BAIAP2L1,CLDN7,CYP27B1,ELF3, ELMO3,EPS8L2,KRT19,PLD2,PODXL2,POLR1C,PPAP2C, PVRL4,RTKN,SAMD10,SLC37A1,SPINT1,TMPRSS13,TTC9 |
B3GNT4,CD164L2,CYB5D1,DPF1,GRIN1,HHIPL2,ICAM5, KREMEN2,LOC153328,MAPK12,METRN,MT1A,MT1E,MT1L, NUDT8,RAC3,RNMTL1,SLC34A3,TLX3,TRABD,TRIM7 | AZIN2,B3GNT4,C14orf178,CEP170P1,CHI3L2,CLRN1,CR1L, CXCL13,DNAJC14,EXD1,HLA-DQA2,HSF5,LOC145474,LOC441454, LOC644669,LOC732275,OR5B2,OTOF,OVCH1,RAD21L1,TSC22D4 |
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 B3GNT4 |
There's no related Drug. |
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Cross referenced IDs for B3GNT4 |
* 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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