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 SLC16A3

Basic gene info.	Gene symbol	SLC16A3
	Gene name	solute carrier family 16 (monocarboxylate transporter), member 3
	Synonyms	MCT 3\|MCT 4\|MCT-3\|MCT-4\|MCT3\|MCT4
	Cytomap	UCSC genome browser: 17q25
	Genomic location	chr17 :80190107-80197375
	Type of gene	protein-coding
	RefGenes	NM_001042422.2, NM_001042423.2,NM_001206950.1,NM_001206951.1,NM_001206952.1, NM_004207.3,
	Ensembl id	ENSG00000141526
	Description	monocarboxylate transporter 3monocarboxylate transporter 4solute carrier family 16 (monocarboxylic acid transporters), member 3solute carrier family 16, member 3 (monocarboxylic acid transporter 4)
	Modification date	20141207
dbXrefs	MIM : 603877
	HGNC : HGNC
	Ensembl : ENSG00000141526
	HPRD : 04854
	Vega : OTTHUMG00000178832
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC16A3
	BioGPS: 9123
	Gene Expression Atlas: ENSG00000141526
	The Human Protein Atlas: ENSG00000141526
Pathway	NCI Pathway Interaction Database: SLC16A3
	KEGG: SLC16A3
	REACTOME: SLC16A3
	ConsensusPathDB
	Pathway Commons: SLC16A3
Metabolism	MetaCyc: SLC16A3
	HUMANCyc: SLC16A3
Regulation	Ensembl's Regulation: ENSG00000141526
	miRBase: chr17 :80,190,107-80,197,375
	TargetScan: NM_001042422
	cisRED: ENSG00000141526
Context	iHOP: SLC16A3
	cancer metabolism search in PubMed: SLC16A3
	UCL Cancer Institute: SLC16A3
Assigned class in ccmGDB	C

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Phenotypic Information for SLC16A3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLC16A3
	Familial Cancer Database: SLC16A3

* 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_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_PYRUVATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: SLC16A3
	MedGen: SLC16A3 (Human Medical Genetics with Condition)
	ClinVar: SLC16A3
Phenotype	MGI: SLC16A3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLC16A3

Mutations for SLC16A3

* 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 SLC16A3 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
AA373754	SLC16A3	1	40	17	80186944	80186983	RNF213	36	222	17	78237458	78247106
AK127090	SLC16A3	1	2846	17	80186921	80189766	FTH1	2839	3621	11	61732038	61734967
AI128892	SLC16A3	1	137	17	80196796	80196935	SLC16A3	133	404	17	80194689	80195226
CB530028	SLC16A3	18	489	17	80196884	80197355	SLC16A3	482	590	17	80195530	80195639

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=12)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr17:80195666-80195666	p.F340L	3
chr17:80195293-80195293	p.R216L	2
chr17:80196735-80196735	p.E427E	2
chr17:80195582-80195582	p.G312G	2
chr17:80196837-80196837	p.P461P	2
chr17:80195519-80195519	p.R291R	1
chr17:80195699-80195699	p.K351N	1
chr17:80195264-80195264	p.P206P	1
chr17:80195528-80195528	p.S294S	1
chr17:80193902-80193902	p.V6V	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				2			1		1			7	4		3
# mutation				1	1				2			1		1			9	4		3
nonsynonymous SNV				1	1				1			1		1			1	3		1
synonymous SNV									1								8	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
chr17:80195756	p.F265F,SLC16A3	1
chr17:80195343	p.F276F,SLC16A3	1
chr17:80196792	p.R291R,SLC16A3	1
chr17:80193902	p.S294S,SLC16A3	1
chr17:80195437	p.V6V,SLC16A3	1
chr17:80196837	p.F300L,SLC16A3	1
chr17:80194035	p.Q51E,SLC16A3	1
chr17:80195441	p.N305N,SLC16A3	1
chr17:80194073	p.I63M,SLC16A3	1
chr17:80195474	p.F340L,SLC16A3	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 SLC16A3 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 SLC16A3

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


ARPC1B,BMP1,CCM2,EMILIN1,EMP3,FAM20C,HHIPL1, KIFC3,LEPRE1,LGALS1,METRNL,MRC2,PCOLCE,PLA2G15, PLAUR,RCN3,SERPINH1,SLC16A3,TMED9,TREM1,UPP1	ACOT11,AKR1B1,CARM1,CCDC28B,DNASE1L1,GMPR,HSPB1, IL32,IMPA2,LINC00116,PKM,PLEC,PPP1R3F,RAMP1, SCN1B,SH2B2,SLC16A3,SNAI3,TEAD4,TPI1,UBAC1

ADM,ALDOA,CDC42EP2,CDCP1,DDIT4,EGLN3,ERO1L, IL1RN,P4HA1,P4HB,PFKFB3,PFKP,PGAM1,PKM, PLOD1,RHOF,SEMA4B,SLC16A3,TMEM92,TNIP1,TRIM47	CNPPD1,EGLN3,ENTPD8,GBA,IFNGR2,KRTAP5-5,LITAF, LOC646627,MAPK3,N4BP1,P2RX4,PEX26,PRSS8,SERINC2, SLC16A3,SLC8B1,SLC6A10P,TJP3,TMEM127,TNIP1,TTC22

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 SLC16A3

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
DB00119	solute carrier family 16, member 3 (monocarboxylic acid transporter 4)	approved; nutraceutical	Pyruvic acid

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Cross referenced IDs for SLC16A3

* 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