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 SLC2A1

Basic gene info.	Gene symbol	SLC2A1
	Gene name	solute carrier family 2 (facilitated glucose transporter), member 1
	Synonyms	DYT17\|DYT18\|DYT9\|EIG12\|GLUT\|GLUT-1\|GLUT1\|GLUT1DS\|HTLVR\|PED
	Cytomap	UCSC genome browser: 1p34.2
	Genomic location	chr1 :43391045-43424847
	Type of gene	protein-coding
	RefGenes	NM_006516.2,
	Ensembl id	ENSG00000117394
	Description	glucose transporter type 1, erythrocyte/brainhepG2 glucose transporterhuman T-cell leukemia virus (I and II) receptorreceptor for HTLV-1 and HTLV-2solute carrier family 2, facilitated glucose transporter member 1
	Modification date	20141222
dbXrefs	MIM : 138140
	MIM : 143090
	HGNC : HGNC
	Ensembl : ENSG00000117394
	HPRD : 00683
	Vega : OTTHUMG00000007657
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC2A1
	BioGPS: 6513
	Gene Expression Atlas: ENSG00000117394
	The Human Protein Atlas: ENSG00000117394
Pathway	NCI Pathway Interaction Database: SLC2A1
	KEGG: SLC2A1
	REACTOME: SLC2A1
	ConsensusPathDB
	Pathway Commons: SLC2A1
Metabolism	MetaCyc: SLC2A1
	HUMANCyc: SLC2A1
Regulation	Ensembl's Regulation: ENSG00000117394
	miRBase: chr1 :43,391,045-43,424,847
	TargetScan: NM_006516
	cisRED: ENSG00000117394
Context	iHOP: SLC2A1
	cancer metabolism search in PubMed: SLC2A1
	UCL Cancer Institute: SLC2A1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SLC2A1 in cancer cell metabolism	1. Ooi AT, Gomperts BN (2015) Molecular Pathways: Targeting Cellular Energy Metabolism in Cancer via Inhibition of SLC2A1 and LDHA. Clin Cancer Res 21: 2440-2444. doi: 10.1158/1078-0432.CCR-14-1209. pmid: 4452440. go to article 2. Grimm M, Munz A, Teriete P, Nadtotschi T, Reinert S (2014) GLUT-1(+)/TKTL1(+) coexpression predicts poor outcome in oral squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 117: 743-753. doi: 10.1016/j.oooo.2014.02.007. go to article 3. Lopez-Serra P, Marcilla M, Villanueva A, Ramos-Fernandez A, Palau A, et al. (2014) A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect. Nat Commun 5: 3608. doi: 10.1038/ncomms4608. pmid: 3988805. go to article 4. Wang YD, Li SJ, Liao JX (2013) Inhibition of glucose transporter 1 (GLUT1) chemosensitized head and neck cancer cells to cisplatin. Technol Cancer Res Treat 12: 525-535. doi: 10.7785/tcrt.2012.500343. go to article

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Phenotypic Information for SLC2A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLC2A1
	Familial Cancer Database: SLC2A1

* 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
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: SLC2A1
	MedGen: SLC2A1 (Human Medical Genetics with Condition)
	ClinVar: SLC2A1
Phenotype	MGI: SLC2A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLC2A1

Mutations for SLC2A1

* 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 SLC2A1 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
AW366615	ACTR1A	1	98	10	104240498	104240595	SLC2A1	93	176	1	43396338	43396424
AW856224	PERP	35	285	6	138413330	138428298	SLC2A1	279	515	1	43393319	43394674
AW352237	SLC2A1	1	89	1	43406854	43406943	ATN1	81	248	12	7047661	7047828
BE828104	BLMH	1	91	17	28576084	28576174	SLC2A1	87	372	1	43406768	43407053

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=26)	Stat. for Synonymous SNVs (# total SNVs=19)

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
chr1:43392858-43392858	p.F445L	3
chr1:43396302-43396302	p.A171T	2
chr1:43396734-43396734	p.F86F	2
chr1:43395437-43395437	p.R232C	2
chr1:43408914-43408914	p.I33L	2
chr1:43396414-43396414	p.C133C	2
chr1:43408966-43408966	p.A15A	2
chr1:43393459-43393459	p.S365S	1
chr1:43396500-43396500	p.V105M	1
chr1:43395282-43395282	p.Q283Q	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=4

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	3	2	1	7	3		2					1	1	2			10	10		7
# mutation	4	2	1	6	3		2					1	1	2			10	10		7
nonsynonymous SNV	3		1	6	2		2					1		2			3	5		3
synonymous SNV	1	2			1								1				7	5		4

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
chr1:43392858	p.F445L	3
chr1:43395437	p.A171T	2
chr1:43396734	p.F86F	2
chr1:43396302	p.R232C	2
chr1:43394969	p.F395F	1
chr1:43396351	p.C201C	1
chr1:43393358	p.R51H	1
chr1:43396814	p.L394L	1
chr1:43395282	p.N45S	1
chr1:43396355	p.P385P	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 SLC2A1 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 SLC2A1

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


ADM,CA9,CDC20,DSG3,DUSP7,FERMT1,GJB3, GJB5,KRT14,KRT16,KRT17,KRT5,KRT6A,KRT6B, MICALL1,NDRG1,PERP,PKP1,SFN,SLC2A1,TRIM29	ANXA9,AP1M2,ATP6V1G1,CDH1,CLDN7,CRB3,DLG3, EZR,FAM83H,HDAC1,HHAT,HN1L,KRT18,LRRC8E, PIP4K2C,SDC1,SLC2A1,SLC35A2,SLC9A3R1,SPINT2,SUSD4

BEAN,ADIRF,C16orf74,CA6,CACNG6,CDA,ELOVL1, EPHA2,EPHB6,GAS6-AS2,GJB3,KLK6,KLK8,PAK7, PAPL,SLC1A5,SLC2A1,SOHLH1,TCHH,TUBB3,ZNF735	ACTG1,B3GNT3,BAIAP2L1,BCL10,CLDN4,DHDDS,EFNB1, FA2H,GAK,KLF4,MIDN,PCSK7,PICK1,SH2B3, SLC2A1,SLC35D1,TMEM2,TMPRSS2,TRIM11,ZDHHC18,ZDHHC5

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 SLC2A1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00318	solute carrier family 2 (facilitated glucose transporter), member 1	illicit; approved	Codeine
DB00295	solute carrier family 2 (facilitated glucose transporter), member 1	approved; investigational	Morphine

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Cross referenced IDs for SLC2A1

* 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