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 SLC19A2
Basic gene info.Gene symbolSLC19A2
Gene namesolute carrier family 19 (thiamine transporter), member 2
SynonymsTC1|THMD1|THT1|THTR1|TRMA
CytomapUCSC genome browser: 1q23.3
Genomic locationchr1 :169433148-169455208
Type of geneprotein-coding
RefGenesNM_006996.2,
Ensembl idENSG00000117479
Descriptionhigh affinity thiamine transporterreduced folate carrier protein (RFC) likesolute carrier family 19 member 2thTr-1thiamine transporter 1
Modification date20141222
dbXrefs MIM : 603941
HGNC : HGNC
Ensembl : ENSG00000117479
HPRD : 04897
Vega : OTTHUMG00000035452
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC19A2
BioGPS: 10560
Gene Expression Atlas: ENSG00000117479
The Human Protein Atlas: ENSG00000117479
PathwayNCI Pathway Interaction Database: SLC19A2
KEGG: SLC19A2
REACTOME: SLC19A2
ConsensusPathDB
Pathway Commons: SLC19A2
MetabolismMetaCyc: SLC19A2
HUMANCyc: SLC19A2
RegulationEnsembl's Regulation: ENSG00000117479
miRBase: chr1 :169,433,148-169,455,208
TargetScan: NM_006996
cisRED: ENSG00000117479
ContextiHOP: SLC19A2
cancer metabolism search in PubMed: SLC19A2
UCL Cancer Institute: SLC19A2
Assigned class in ccmGDBC

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Phenotypic Information for SLC19A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC19A2
Familial Cancer Database: SLC19A2
* 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: SLC19A2
MedGen: SLC19A2 (Human Medical Genetics with Condition)
ClinVar: SLC19A2
PhenotypeMGI: SLC19A2 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC19A2

Mutations for SLC19A2
* 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 SLC19A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
H59323SLC19A21431169441478169441520THAP7-AS137456222135683421357245
BE177610SLC19A223521169434289169434644EIF2S3347525X2408620224089828

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  1
GAIN (# sample)             1  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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=2)
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
chr1:169446534-169446534p.S222S2
chr1:169438017-169438017p.E363G2
chr1:169446809-169446809p.Y131fs*452
chr1:169446476-169446476p.P242S1
chr1:169437456-169437456p.Y420H1
chr1:169446651-169446651p.A183A1
chr1:169439231-169439231p.G334V1
chr1:169446940-169446940p.P87L1
chr1:169446482-169446482p.D240Y1
chr1:169437459-169437459p.R419C1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 5  3    122  75 5
# mutation11 5  3    122  85 6
nonsynonymous SNV11 3  3    122  45 6
synonymous SNV   2            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
chr1:169446719p.E321D1
chr1:169439219p.V180V1
chr1:169446466p.W320R1
chr1:169446766p.R162Q1
chr1:169439227p.V313A1
chr1:169446468p.C161G1
chr1:169446778p.W301R1
chr1:169439231p.I145T1
chr1:169446469p.S291S1
chr1:169446830p.Y141C1

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 SLC19A2 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 SLC19A2

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

BLZF1,CDK17,CLASP2,ERBB3,EXOC6,FAM134B,FOXA1,
FSIP1,FUT8,FAM214A,CERS6,MARVELD2,PCBD2,RABEP1,
RALGAPA1,RALGPS2,RCOR3,SLC19A2,SLC22A5,TBC1D9,THSD4
CFAP126,CPEB4,CUL3,DYNC1LI1,G3BP2,GFM1,KLF9,
L2HGDH,MAPK6,MLF1,MUM1L1,NPEPPS,OXNAD1,PTP4A1,
RAB21,RNF115,SAR1B,SLC19A2,TP53INP2,UBE3A,USP38

ABCB10,C1orf112,SPRTN,C1orf43,GPATCH2,MRPL9,POLR3C,
RFWD2,SLC19A2,SMYD2,SNRPE,TADA1,TBCE,TFB2M,
TIPRL,TMEM206,TOMM20,TSEN15,TSNAX,UFC1,VPS72
VCPKMT,CCDC173,CCNL1,CEBPB,CSRNP1,DCUN1D3,GJA1,
IGFBP1,IL6,JMJD6,KLF9,MAK,ODF3L1,PDK4,
PRPF4B,RBM39,SCNN1G,SLC19A2,TIPARP,TSC22D3,ZNF460
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 SLC19A2
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
DB00152solute carrier family 19 (thiamine transporter), member 2approved; nutraceuticalThiamine


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Cross referenced IDs for SLC19A2
* 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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