Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	GALT
	Gene name	galactose-1-phosphate uridylyltransferase
	Synonyms	-
	Cytomap	UCSC genome browser: 9p13
	Genomic location	chr9 :34646585-34650595
	Type of gene	protein-coding
	RefGenes	NM_000155.3, NM_001258332.1,
	Ensembl id	ENSG00000213930
	Description	UDP-glucose--hexose-1-phosphate uridylyltransferasegal-1-P uridylyltransferasegalactose-1-phosphate uridyl transferase
	Modification date	20141219
dbXrefs	MIM : 606999
	HGNC : HGNC
	Ensembl : ENSG00000213930
	HPRD : 06106
Protein	UniProt: P07902 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GALT
	BioGPS: 2592
	Gene Expression Atlas: ENSG00000213930
	The Human Protein Atlas: ENSG00000213930
Pathway	NCI Pathway Interaction Database: GALT
	KEGG: GALT
	REACTOME: GALT
	ConsensusPathDB
	Pathway Commons: GALT
Metabolism	MetaCyc: GALT
	HUMANCyc: GALT
Regulation	Ensembl's Regulation: ENSG00000213930
	miRBase: chr9 :34,646,585-34,650,595
	TargetScan: NM_000155
	cisRED: ENSG00000213930
Context	iHOP: GALT
	cancer metabolism search in PubMed: GALT
	UCL Cancer Institute: GALT
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GALT in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_GALACTOSE_METABOLISM KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	230400; phenotype. 230400; phenotype. 606999; gene. 606999; gene.
Orphanet	79239; Classic galactosemia. 79239; Classic galactosemia.
Disease	KEGG Disease: GALT
	MedGen: GALT (Human Medical Genetics with Condition)
	ClinVar: GALT
Phenotype	MGI: GALT (International Mouse Phenotyping Consortium)
Phenotype	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.

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 GALT 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
CV351576	SNRNP70	1	116	19	49611334	49611448	GALT	110	377	9	34648372	34649047
BF593407	GALT	1	307	9	34650038	34650571	CENPF	303	361	1	214786559	214786617

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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Somatic 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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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
chr9:34646773-34646773	p.F24L	2
chr9:34649061-34649061	p.Y296C	2
chr9:34647078-34647078	p.?	2
chr9:34648859-34648859	p.R263Q	2
chr9:34649050-34649050	p.T292T	1
chr9:34647856-34647856	p.S135S	1
chr9:34650388-34650388	p.L361P	1
chr9:34648454-34648454	p.?	1
chr9:34646774-34646774	p.R25R	1
chr9:34647884-34647884	p.P145T	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		3			1		3			3	2	1			4	1	2	4
# mutation	1	1		3			1		3			3	2	1			4	2	2	5
nonsynonymous SNV	1	1		3			1		2			2	1	1			1	1	2	3
synonymous SNV									1			1	1				3	1		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
chr9:34646774	p.E128Q,GALT	1
chr9:34647938	p.R25R	1
chr9:34649475	p.P135L,GALT	1
chr9:34647203	p.R67H	1
chr9:34648148	p.R153W,GALT	1
chr9:34649478	p.V85V	1
chr9:34647491	p.R154W,GALT	1
chr9:34648368	p.D113D	1
chr9:34649520	p.E162D,GALT	1
chr9:34647664	p.H114Y	1

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA28548; -.
Organism-specific databases	PharmGKB	PA28548; -.
Organism-specific databases	CTD	2592; -.
Organism-specific databases	CTD	2592; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01861	galactose-1-phosphate uridylyltransferase	experimental	Glucose-Uridine-C1,5'-Diphosphate
DB03435	galactose-1-phosphate uridylyltransferase	experimental	Uridine-5'-Diphosphate
DB03685	galactose-1-phosphate uridylyltransferase	experimental	Uridine-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