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 symbolSLC16A3
Gene namesolute carrier family 16 (monocarboxylate transporter), member 3
SynonymsMCT 3|MCT 4|MCT-3|MCT-4|MCT3|MCT4
CytomapUCSC genome browser: 17q25
Genomic locationchr17 :80190107-80197375
Type of geneprotein-coding
RefGenesNM_001042422.2,
NM_001042423.2,NM_001206950.1,NM_001206951.1,NM_001206952.1,
NM_004207.3,
Ensembl idENSG00000141526
Descriptionmonocarboxylate transporter 3monocarboxylate transporter 4solute carrier family 16 (monocarboxylic acid transporters), member 3solute carrier family 16, member 3 (monocarboxylic acid transporter 4)
Modification date20141207
dbXrefs MIM : 603877
HGNC : HGNC
Ensembl : ENSG00000141526
HPRD : 04854
Vega : OTTHUMG00000178832
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC16A3
BioGPS: 9123
Gene Expression Atlas: ENSG00000141526
The Human Protein Atlas: ENSG00000141526
PathwayNCI Pathway Interaction Database: SLC16A3
KEGG: SLC16A3
REACTOME: SLC16A3
ConsensusPathDB
Pathway Commons: SLC16A3
MetabolismMetaCyc: SLC16A3
HUMANCyc: SLC16A3
RegulationEnsembl's Regulation: ENSG00000141526
miRBase: chr17 :80,190,107-80,197,375
TargetScan: NM_001042422
cisRED: ENSG00000141526
ContextiHOP: SLC16A3
cancer metabolism search in PubMed: SLC16A3
UCL Cancer Institute: SLC16A3
Assigned class in ccmGDBC

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Phenotypic Information for SLC16A3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE
REACTOME_PYRUVATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC16A3
MedGen: SLC16A3 (Human Medical Genetics with Condition)
ClinVar: SLC16A3
PhenotypeMGI: SLC16A3 (International Mouse Phenotyping Consortium)
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.

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 SLC16A3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA373754SLC16A3140178018694480186983RNF21336222177823745878247106
AK127090SLC16A312846178018692180189766FTH128393621116173203861734967
AI128892SLC16A31137178019679680196935SLC16A3133404178019468980195226
CB530028SLC16A318489178019688480197355SLC16A3482590178019553080195639

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=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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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
chr17:80195666-80195666p.F340L3
chr17:80195293-80195293p.R216L2
chr17:80196735-80196735p.E427E2
chr17:80195582-80195582p.G312G2
chr17:80196837-80196837p.P461P2
chr17:80195264-80195264p.P206P1
chr17:80195528-80195528p.S294S1
chr17:80193902-80193902p.V6V1
chr17:80195756-80195756p.G370G1
chr17:80195544-80195544p.F300L1

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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
# sample   11   2  1 1  74 3
# mutation   11   2  1 1  94 3
nonsynonymous SNV   11   1  1 1  13 1
synonymous SNV        1       81 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
chr17:80195343p.V6V,SLC16A31
chr17:80196792p.F300L,SLC16A31
chr17:80193902p.Q51E,SLC16A31
chr17:80195437p.N305N,SLC16A31
chr17:80196837p.I63M,SLC16A31
chr17:80194035p.F340L,SLC16A31
chr17:80195441p.G73G,SLC16A31
chr17:80194073p.A366V,SLC16A31
chr17:80195474p.G75D,SLC16A31
chr17:80194103p.G370G,SLC16A31

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 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

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

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
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 SLC16A3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00119solute carrier family 16, member 3 (monocarboxylic acid transporter 4)approved; nutraceuticalPyruvic 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



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