Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for GXYLT2
Basic gene info.Gene symbolGXYLT2
Gene nameglucoside xylosyltransferase 2
SynonymsGLT8D4
CytomapUCSC genome browser: 3p13
Genomic locationchr3 :72937384-73024522
Type of geneprotein-coding
RefGenesNM_001080393.1,
Ensembl idENSG00000172986
Descriptionglycosyltransferase 8 domain containing 4glycosyltransferase 8 domain-containing protein 4
Modification date20141207
dbXrefs MIM : 613322
HGNC : HGNC
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GXYLT2
BioGPS: 727936
Gene Expression Atlas: ENSG00000172986
The Human Protein Atlas: ENSG00000172986
PathwayNCI Pathway Interaction Database: GXYLT2
KEGG: GXYLT2
REACTOME: GXYLT2
ConsensusPathDB
Pathway Commons: GXYLT2
MetabolismMetaCyc: GXYLT2
HUMANCyc: GXYLT2
RegulationEnsembl's Regulation: ENSG00000172986
miRBase: chr3 :72,937,384-73,024,522
TargetScan: NM_001080393
cisRED: ENSG00000172986
ContextiHOP: GXYLT2
cancer metabolism search in PubMed: GXYLT2
UCL Cancer Institute: GXYLT2
Assigned class in ccmGDBC

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Phenotypic Information for GXYLT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GXYLT2
Familial Cancer Database: GXYLT2
* This gene is included in those cancer gene databases.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GXYLT2
MedGen: GXYLT2 (Human Medical Genetics with Condition)
ClinVar: GXYLT2
PhenotypeMGI: GXYLT2 (International Mouse Phenotyping Consortium)
PhenomicDB: GXYLT2

Mutations for GXYLT2
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GXYLT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1 1  1   
GAIN (# sample)          1  1   
LOSS (# sample)        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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr3:72957598-72957598p.N119S2
chr3:72971480-72971480p.F198F2
chr3:72957696-72957696p.E152K2
chr3:73004380-73004380p.H244H2
chr3:73004496-73004496p.F283S2
chr3:72971411-72971411p.I175I2
chr3:73016753-73016753p.Y344Y2
chr3:73006438-73006438p.K304R2
chr3:73006469-73006469p.Q314Q1
chr3:73016808-73016808p.R363*1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 8  3 11 14   52 7
# mutation41 8  3 11 14   52 8
nonsynonymous SNV4  4  2 11 13   31 6
synonymous SNV 1 4  1     1   21 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr3:72957696p.E152K2
chr3:72971411p.I175I2
chr3:73016867p.K248N1
chr3:72957678p.R382R1
chr3:73004291p.E146K1
chr3:73006469p.I249F1
chr3:73024140p.D388N1
chr3:72957687p.L149V1
chr3:73004303p.M273I1
chr3:73016739p.L390I1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for GXYLT2 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 GXYLT2

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

ADAM12,ASPN,BNC2,C14orf37,CDH11,COL3A1,COL5A2,
DCN,FAM26E,FBN1,GXYLT2,HMCN1,LRRC15,MXRA5,
RASGRF2,RECK,SGCD,SLC24A2,ST6GAL2,THBS2,VCAN
ADAMTSL1,BNC2,C14orf37,CDON,COL6A3,CORO2B,DCLK1,
ENPEP,FAT4,GXYLT2,HMCN1,KDELC2,LPAR1,NID1,
OLFML1,PCDH18,PDGFRB,RECK,RFTN2,RNF144A,TPST1

ATXN1,CCDC80,CXCL12,EFEMP1,F13A1,FBN1,GXYLT2,
LAMB1,LIN7A,LMCD1,MAST4,NRP2,PPAP2B,RGS4,
SH3BP4,SH3BP5,SVEP1,THBS1,TMEM150C,VCAN,ZNF362
ASAP3,B4GALNT2,COLCA2,APMAP,CCNJL,EDA,EHHADH,
EPB41L1,GXYLT2,HMGCS2,HOXB6,HOXB8,KCNE2,KCNV1,
KREMEN1,LRPPRC,NAALADL2,PKHD1,SCUBE2,TBC1D4,VGLL4
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for GXYLT2


There's no related Drug.
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Cross referenced IDs for GXYLT2
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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