Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 GALE
Basic gene info.Gene symbolGALE
Gene nameUDP-galactose-4-epimerase
SynonymsSDR1E1
CytomapUCSC genome browser: 1p36-p35
Genomic locationchr1 :24122088-24127294
Type of geneprotein-coding
RefGenesNM_000403.3,
NM_001008216.1,NM_001127621.1,
Ensembl idENSG00000117308
DescriptionUDP galactose-4'-epimeraseUDP-GalNAc 4-epimeraseUDP-GlcNAc 4-epimeraseUDP-N-acetylgalactosamine 4-epimeraseUDP-N-acetylglucosamine 4-epimeraseUDP-galactose 4-epimeraseUDP-glucose 4-epimerasegalactose-4-epimerase, UDP-galactowaldenaseshort chain d
Modification date20141219
dbXrefs MIM : 606953
HGNC : HGNC
Ensembl : ENSG00000117308
HPRD : 06092
Vega : OTTHUMG00000002958
ProteinUniProt: Q14376
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALE
BioGPS: 2582
Gene Expression Atlas: ENSG00000117308
The Human Protein Atlas: ENSG00000117308
PathwayNCI Pathway Interaction Database: GALE
KEGG: GALE
REACTOME: GALE
ConsensusPathDB
Pathway Commons: GALE
MetabolismMetaCyc: GALE
HUMANCyc: GALE
RegulationEnsembl's Regulation: ENSG00000117308
miRBase: chr1 :24,122,088-24,127,294
TargetScan: NM_000403
cisRED: ENSG00000117308
ContextiHOP: GALE
cancer metabolism search in PubMed: GALE
UCL Cancer Institute: GALE
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GALE in cancer cell metabolism1. Bauer CH, Buchsel R, Morris HP, Reutter WG (1980) Alterations of D-galactose metabolism in Morris hepatomas. Cancer Res 40: 2026-2032. go to article
2. Cramer DW, Greenberg ER, Titus-Ernstoff L, Liberman RF, Welch WR, et al. (2000) A case-control study of galactose consumption and metabolism in relation to ovarian cancer. Cancer Epidemiol Biomarkers Prev 9: 95-101. go to article
3. Ruffing AM, Chen RR (2010) Metabolic engineering of Agrobacterium sp. strain ATCC 31749 for production of an alpha-Gal epitope. Microb Cell Fact 9: 1. doi: 10.1186/1475-2859-9-1. pmid: 2818619. go to article

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Phenotypic Information for GALE(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALE
Familial Cancer Database: GALE
* 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
KEGG_GALACTOSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 230350; phenotype.
606953; gene.
Orphanet 308473; Erythrocyte galactose epimerase deficiency.
308487; Generalized galactose epimerase deficiency.
DiseaseKEGG Disease: GALE
MedGen: GALE (Human Medical Genetics with Condition)
ClinVar: GALE
PhenotypeMGI: GALE (International Mouse Phenotyping Consortium)
PhenomicDB: GALE

Mutations for GALE
* 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 GALE 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
There's no copy number variation information in COSMIC data for this gene.

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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=20)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr1:24124603-24124603p.?2
chr1:24124608-24124608p.E117G2
chr1:24123528-24123528p.S213F2
chr1:24125170-24125170p.R58C1
chr1:24123370-24123370p.G235G1
chr1:24122443-24122443p.A348G1
chr1:24125173-24125173p.G57C1
chr1:24124627-24124627p.G111R1
chr1:24122689-24122689p.A314T1
chr1:24125202-24125202p.E47V1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  72  111 112  41 3
# mutation2  72  111 112  41 3
nonsynonymous SNV1  32   11 112  11 1
synonymous SNV1  4   1        3  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
chr1:24125169p.R300Q,GALE1
chr1:24124297p.E96K,GALE1
chr1:24125170p.G289W,GALE1
chr1:24122442p.G95G,GALE1
chr1:24124334p.T271T,GALE1
chr1:24125202p.A84A,GALE1
chr1:24122730p.R256R,GALE1
chr1:24124347p.R58H,GALE1
chr1:24125210p.G235G,GALE1
chr1:24123007p.R58C,GALE1

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 GALE 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 GALE

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

AKR1A1,ATP6V0C,ATPIF1,BOLA2,SLIRP,PAGR1,GALE,
GFER,LYPLA2,LYPLA2P1,MRPS34,NDUFB10,NMRAL1,PARK7,
PPP4C,RNF181,MSRB1,SNRNP25,TRPT1,TXNDC17,WIBG
ABHD11,CACFD1,CLDN7,COASY,COMT,CYB561,EBP,
FBXL6,GALE,GMPPA,SLC52A2,GSS,IGSF8,MFSD7,
PYCR1,PYCRL,RHPN1,SLC35A2,SLC37A1,ST14,TMED3

ATPIF1,PITHD1,MINOS1,KDF1,COX8A,GALE,CPTP,
GSTK1,HMGCL,LDLRAP1,LYPLA2,LYPLA2P1,PQLC2,RPS6KA1,
SDHB,SH3BGRL3,SLC22A18,SLC22A18AS,TMEM53,TMEM54,ZNF593
ARF1,ARPC1A,CYB561D2,ERP44,GALE,GMPPA,GNG5,
GOLGA5,H2AFY,HDAC1,KCNK1,LXN,MAPKAPK5,MED8,
S100A6,VIMP,SH3BGRL3,SLC35A2,TFF1,TFG,TMED9
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 GALE
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q14376; -.
ChemistryChEMBL CHEMBL5843; -.
Organism-specific databasesPharmGKB PA28531; -.
Organism-specific databasesCTD 2582; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01861UDP-galactose-4-epimeraseexperimentalGlucose-Uridine-C1,5'-Diphosphate
DB01907UDP-galactose-4-epimeraseexperimentalNicotinamide-Adenine-Dinucleotide
DB02196UDP-galactose-4-epimeraseexperimentalUridine-Diphosphate-N-Acetylgalactosamine
DB03095UDP-galactose-4-epimeraseexperimentalTetramethylammonium Ion
DB03397UDP-galactose-4-epimeraseexperimentalUridine-Diphosphate-N-Acetylglucosamine
DB03501UDP-galactose-4-epimeraseexperimentalUridine Diphosphate Galactose
DB04355UDP-galactose-4-epimeraseexperimentalUridine-5'-Monophosphate Glucopyranosyl-Monophosphateester
DB02421UDP-galactose-4-epimeraseexperimentalUridine-5'-Diphosphate-Mannose
DB02790UDP-galactose-4-epimeraseexperimentalPhenyl-Uridine-5'-Diphosphate
DB03435UDP-galactose-4-epimeraseexperimentalUridine-5'-Diphosphate
DB04097UDP-galactose-4-epimeraseexperimentalUridine-5'-Diphosphate-4-Deoxy-4-Fluoro-Alpha-D-Galactose


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Cross referenced IDs for GALE
* 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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