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 SLC19A3
Basic gene info.Gene symbolSLC19A3
Gene namesolute carrier family 19 (thiamine transporter), member 3
SynonymsBBGD|THMD2|THTR2
CytomapUCSC genome browser: 2q37
Genomic locationchr2 :228549925-228582745
Type of geneprotein-coding
RefGenesNM_025243.3,
Ensembl idENSG00000135917
Descriptionsolute carrier family 19, member 3thTr-2thiamine transporter 2
Modification date20141222
dbXrefs MIM : 606152
HGNC : HGNC
Ensembl : ENSG00000135917
HPRD : 07311
Vega : OTTHUMG00000133185
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC19A3
BioGPS: 80704
Gene Expression Atlas: ENSG00000135917
The Human Protein Atlas: ENSG00000135917
PathwayNCI Pathway Interaction Database: SLC19A3
KEGG: SLC19A3
REACTOME: SLC19A3
ConsensusPathDB
Pathway Commons: SLC19A3
MetabolismMetaCyc: SLC19A3
HUMANCyc: SLC19A3
RegulationEnsembl's Regulation: ENSG00000135917
miRBase: chr2 :228,549,925-228,582,745
TargetScan: NM_025243
cisRED: ENSG00000135917
ContextiHOP: SLC19A3
cancer metabolism search in PubMed: SLC19A3
UCL Cancer Institute: SLC19A3
Assigned class in ccmGDBC

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Phenotypic Information for SLC19A3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC19A3
Familial Cancer Database: SLC19A3
* 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_METABOLISM_OF_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC19A3
MedGen: SLC19A3 (Human Medical Genetics with Condition)
ClinVar: SLC19A3
PhenotypeMGI: SLC19A3 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC19A3

Mutations for SLC19A3
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySLC19A3chr2228554646228554666chr128596752085967540
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC19A3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample      1          
GAIN (# sample)      1          
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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=2)
There's no deleted 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
chr2:228563888-228563888p.S181S4
chr2:228563707-228563707p.G242R2
chr2:228552892-228552892p.V435A2
chr2:228563794-228563794p.V213M2
chr2:228552188-228552188p.S472S2
chr2:228564158-228564158p.I91I2
chr2:228563510-228563510p.A307A2
chr2:228552263-228552263p.A447A2
chr2:228564076-228564076p.A119T2
chr2:228564079-228564079p.A118T2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 21101 8 5  9 21 69 11
# mutation 2181 8 5  10 21 610 12
nonsynonymous SNV 1131 7 5  7 1  39 8
synonymous SNV 1 5  1    3 11 31 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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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
chr2:228564158p.I91I3
chr2:228563705p.G242G2
chr2:228563707p.G242R2
chr2:228560704p.A447A2
chr2:228552263p.F189F2
chr2:228563864p.G358D2
chr2:228552899p.M492I1
chr2:228563937p.A357S1
chr2:228560794p.S251S1
chr2:228564115p.V116V1

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 SLC19A3 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 SLC19A3

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

ACVR1C,ADH1A,ADH1B,ADIPOQ,AOC3,AQP7,AQP7P1,
AQPEP,C14orf180,CIDEC,GPD1,GYG2,HEPACAM,HEPN1,
KCNIP2,KLB,LIPE,LOC283392,PLIN1,SLC19A3,TMEM132C
ABHD15,ACACB,ACSS3,ACVR1C,ADH1A,ADH1B,ANKRD53,
ANTXR2,CIDEA,CNTFR,EIF4EBP2,GHR,GNAI1,GYG2,
LOC283392,LOC401052,MAOA,PECR,SLC19A3,TJP2,TMEM132C

ACE2,TMEM252,DGAT2,GET4,GGH,GPR143,IHH,
LOC148709,LOC400794,NODAL,PIGU,PLA2G12B,PLIN2,QPRT,
REEP1,SLC19A3,SLC1A7,SLC2A8,SLC5A6,TSPAN6,VAV3
ACVR1C,ADH6,AGFG2,ALDH18A1,DTX4,EFTUD1,EPB41L4B,
ERBB3,FAM134A,FZD5,HSD17B2,MYO1D,NDRG1,PAQR5,
PLD1,PROSC,RETSAT,RMND5A,SLC19A3,SLC41A2,SOS2
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 SLC19A3
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
DB00151solute carrier family 19, member 3approved; nutraceuticalL-Cysteine
DB00997solute carrier family 19, member 3approved; investigationalDoxorubicin


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Cross referenced IDs for SLC19A3
* 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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