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 SLC19A1
Basic gene info.Gene symbolSLC19A1
Gene namesolute carrier family 19 (folate transporter), member 1
SynonymsCHMD|FOLT|IFC1|REFC|RFC1
CytomapUCSC genome browser: 21q22.3
Genomic locationchr21 :46934628-46962385
Type of geneprotein-coding
RefGenesNM_001205206.1,
NM_001205207.1,NM_194255.2,NM_003056.2,
Ensembl idENSG00000173638
DescriptionIFC-1RFCfolate transporter 1intestinal folate carrier 1placental folate transporterreduced folate carrier proteinsolute carrier family 19 member 1
Modification date20141212
dbXrefs MIM : 600424
HGNC : HGNC
Ensembl : ENSG00000173638
HPRD : 02691
Vega : OTTHUMG00000090397
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC19A1
BioGPS: 6573
Gene Expression Atlas: ENSG00000173638
The Human Protein Atlas: ENSG00000173638
PathwayNCI Pathway Interaction Database: SLC19A1
KEGG: SLC19A1
REACTOME: SLC19A1
ConsensusPathDB
Pathway Commons: SLC19A1
MetabolismMetaCyc: SLC19A1
HUMANCyc: SLC19A1
RegulationEnsembl's Regulation: ENSG00000173638
miRBase: chr21 :46,934,628-46,962,385
TargetScan: NM_001205206
cisRED: ENSG00000173638
ContextiHOP: SLC19A1
cancer metabolism search in PubMed: SLC19A1
UCL Cancer Institute: SLC19A1
Assigned class in ccmGDBC

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Phenotypic Information for SLC19A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC19A1
Familial Cancer Database: SLC19A1
* 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: SLC19A1
MedGen: SLC19A1 (Human Medical Genetics with Condition)
ClinVar: SLC19A1
PhenotypeMGI: SLC19A1 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC19A1

Mutations for SLC19A1
* 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 SLC19A1 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
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=12)
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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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
chr21:46951556-46951556p.P232P5
chr21:46957794-46957794p.H27R4
chr21:46950811-46950811p.V342I2
chr21:46945797-46945797p.I409I1
chr21:46951701-46951701p.T184M1
chr21:46951324-46951324p.D310N1
chr21:46951971-46951971p.P94L1
chr21:46935678-46935678p.E557V1
chr21:46951464-46951464p.R263Q1
chr21:46945798-46945798p.I409T1

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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
# sample31 51 4 2  2    63 11
# mutation31 61 5 2  2    64 12
nonsynonymous SNV21 61 1 1  1    43 9
synonymous SNV1     4 1  1    21 3
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
chr21:46951414p.G240S,SLC19A12
chr21:46950811p.T368A,SLC19A11
chr21:46951984p.E217K,SLC19A11
chr21:46951439p.L61L,SLC19A11
chr21:46935726p.L358L,SLC19A11
chr21:46951701p.R203R,SLC19A11
chr21:46950869p.P54L,SLC19A11
chr21:46957703p.A357T,SLC19A11
chr21:46951450p.A201T,SLC19A11
chr21:46935892p.P54S,SLC19A11

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 SLC19A1 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 SLC19A1

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

BOP1,C20orf27,C21orf33,FAM207A,DAZAP1,EXOSC4,FBXL6,
SLC52A2,TONSL,PFKL,PRR7,PUF60,PWP2,RECQL4,
RRP1,RRP9,SLC19A1,TIGD5,U2AF1,VARS,WDR4
ACY1,BCAP31,BOK,DGAT1,IMPDH1,KLHL22,LPHN1,
LRP3,PDXK,PIGS,PLEKHG6,POLR2E,POR,SCRN2,
SLC19A1,SLC25A10,TALDO1,TMEM53,TST,TUBG1,TYSND1

ATAD3A,FAM207A,HGH1,DAZAP1,DDX51,DOHH,LONP1,
NCLN,TONSL,NOC4L,PUS1,PWP2,RRP12,RRP1,
RRP1B,SLC19A1,SRM,TMEM201,TRAP1,U2AF1,WDR4
ABHD15,ACAD10,ACADS,ACO2,ACSF3,ADH6,AFG3L2,
FAM213B,SLC52A3,CEBPA,CLPTM1,CMBL,DQX1,EPHA1,
GJB1,KBTBD11,PAQR5,PFKL,SLC19A1,SPNS1,TMEM19
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 SLC19A1
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
DB01234solute carrier family 19 (folate transporter), member 1approved; investigationalDexamethasone
DB00515solute carrier family 19 (folate transporter), member 1approvedCisplatin
DB00531solute carrier family 19 (folate transporter), member 1approved; investigationalCyclophosphamide
DB00970solute carrier family 19 (folate transporter), member 1approvedDactinomycin
DB00997solute carrier family 19 (folate transporter), member 1approved; investigationalDoxorubicin
DB01611solute carrier family 19 (folate transporter), member 1approvedHydroxychloroquine
DB00795solute carrier family 19 (folate transporter), member 1approvedSulfasalazine
DB00145solute carrier family 19 (folate transporter), member 1approved; nutraceuticalGlycine
DB00133solute carrier family 19 (folate transporter), member 1approved; nutraceuticalL-Serine
DB00293solute carrier family 19 (folate transporter), member 1approved; investigationalRaltitrexed
DB00158solute carrier family 19 (folate transporter), member 1approved; nutraceuticalFolic Acid
DB00987solute carrier family 19 (folate transporter), member 1approved; investigationalCytarabine
DB00694solute carrier family 19 (folate transporter), member 1approvedDaunorubicin
DB00773solute carrier family 19 (folate transporter), member 1approvedEtoposide
DB00650solute carrier family 19 (folate transporter), member 1approvedLeucovorin
DB01033solute carrier family 19 (folate transporter), member 1approvedMercaptopurine
DB00563solute carrier family 19 (folate transporter), member 1approvedMethotrexate
DB00635solute carrier family 19 (folate transporter), member 1approvedPrednisone
DB00541solute carrier family 19 (folate transporter), member 1approved; investigationalVincristine
DB00544solute carrier family 19 (folate transporter), member 1approvedFluorouracil
DB00762solute carrier family 19 (folate transporter), member 1approved; investigationalIrinotecan
DB00958solute carrier family 19 (folate transporter), member 1approvedCarboplatin
DB00642solute carrier family 19 (folate transporter), member 1approved; investigationalPemetrexed


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Cross referenced IDs for SLC19A1
* 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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