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 GALT
Basic gene info.Gene symbolGALT
Gene namegalactose-1-phosphate uridylyltransferase
Synonyms-
CytomapUCSC genome browser: 9p13
Genomic locationchr9 :34646585-34650595
Type of geneprotein-coding
RefGenesNM_000155.3,
NM_001258332.1,
Ensembl idENSG00000213930
DescriptionUDP-glucose--hexose-1-phosphate uridylyltransferasegal-1-P uridylyltransferasegalactose-1-phosphate uridyl transferase
Modification date20141219
dbXrefs MIM : 606999
HGNC : HGNC
Ensembl : ENSG00000213930
HPRD : 06106
ProteinUniProt: P07902
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALT
BioGPS: 2592
Gene Expression Atlas: ENSG00000213930
The Human Protein Atlas: ENSG00000213930
PathwayNCI Pathway Interaction Database: GALT
KEGG: GALT
REACTOME: GALT
ConsensusPathDB
Pathway Commons: GALT
MetabolismMetaCyc: GALT
HUMANCyc: GALT
RegulationEnsembl's Regulation: ENSG00000213930
miRBase: chr9 :34,646,585-34,650,595
TargetScan: NM_000155
cisRED: ENSG00000213930
ContextiHOP: GALT
cancer metabolism search in PubMed: GALT
UCL Cancer Institute: GALT
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GALT in cancer cell metabolism1. Gatto F, Miess H, Schulze A, Nielsen J (2015) Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism. Sci Rep 5: 10738. doi: 10.1038/srep10738. go to article

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Phenotypic Information for GALT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALT
Familial Cancer Database: GALT
* 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 230400; phenotype.
230400; phenotype.
606999; gene.
606999; gene.
Orphanet 79239; Classic galactosemia.
79239; Classic galactosemia.
DiseaseKEGG Disease: GALT
MedGen: GALT (Human Medical Genetics with Condition)
ClinVar: GALT
PhenotypeMGI: GALT (International Mouse Phenotyping Consortium)
PhenomicDB: GALT

Mutations for GALT
* 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 GALT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV351576SNRNP701116194961133449611448GALT11037793464837234649047
BF593407GALT130793465003834650571CENPF3033611214786559214786617

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr9:34646773-34646773p.F24L2
chr9:34649061-34649061p.Y296C2
chr9:34647078-34647078p.?2
chr9:34648859-34648859p.R263Q2
chr9:34649050-34649050p.T292T1
chr9:34647856-34647856p.S135S1
chr9:34650388-34650388p.L361P1
chr9:34648454-34648454p.?1
chr9:34646774-34646774p.R25R1
chr9:34647884-34647884p.P145T1

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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
# sample11 3  1 3  321  4124
# mutation11 3  1 3  321  4225
nonsynonymous SNV11 3  1 2  211  1123
synonymous SNV        1  11   31 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
chr9:34646774p.E128Q,GALT1
chr9:34647938p.R25R1
chr9:34649475p.P135L,GALT1
chr9:34647203p.R67H1
chr9:34648148p.R153W,GALT1
chr9:34649478p.V85V1
chr9:34647491p.R154W,GALT1
chr9:34648368p.D113D1
chr9:34649520p.E162D,GALT1
chr9:34647664p.H114Y1

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 GALT 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 GALT

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

ARHGEF39,RPP25L,CCDC107,CLTA,DCTN3,DEF6,FAM3A,
FANCG,GALT,GRHPR,HLA-F,IL11RA,LEMD2,MAD1L1,
NDUFB6,PSAPL1,NELFE,SIGMAR1,STOML2,TESK1,TPRA1
BCS1L,COX4I1,CPSF3L,FRS3,GALT,HSF1,MIIP,
MRPS2,NPRL3,PLEKHJ1,POLL,PRMT7,RFNG,RPL37A,
SDR39U1,SLC27A1,SPSB3,TAZ,PAM16,TJAP1,UCKL1

C1orf64,TMEM261,RPP25L,CDK10,COQ4,CPSF3L,FANCG,
GALT,GRHPR,GYPB,HDAC10,HIST1H4G,IGDCC3,KIF12,
LCN12,OC90,OR6C68,SH3GLB2,SIGMAR1,SNAR-F,TMCO6
ACY3,SLC25A47,DAK,DNASE1,EMB,FAM151A,FOXD1,
GALT,HSD17B3,KDM8,LOC647121,MAF,MLXIPL,MMEL1,
MST1,PFKFB4,PLB1,SAT2,TM4SF5,TMED4,TMPRSS7
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 GALT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28548; -.
Organism-specific databasesPharmGKB PA28548; -.
Organism-specific databasesCTD 2592; -.
Organism-specific databasesCTD 2592; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01861galactose-1-phosphate uridylyltransferaseexperimentalGlucose-Uridine-C1,5'-Diphosphate
DB03435galactose-1-phosphate uridylyltransferaseexperimentalUridine-5'-Diphosphate
DB03685galactose-1-phosphate uridylyltransferaseexperimentalUridine-5'-Monophosphate


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Cross referenced IDs for GALT
* 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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