Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 DHFR
Basic gene info.Gene symbolDHFR
Gene namedihydrofolate reductase
SynonymsDHFRP1|DYR
CytomapUCSC genome browser: 5q11.2-q13.2
Genomic locationchr5 :79922044-79950800
Type of geneprotein-coding
RefGenesNM_000791.3,
NM_001290354.1,NM_001290357.1,NR_110936.1,
Ensembl idENSG00000228716
Description-
Modification date20141207
dbXrefs MIM : 126060
HGNC : HGNC
Ensembl : ENSG00000228716
HPRD : 00519
Vega : OTTHUMG00000162529
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DHFR
BioGPS: 1719
Gene Expression Atlas: ENSG00000228716
The Human Protein Atlas: ENSG00000228716
PathwayNCI Pathway Interaction Database: DHFR
KEGG: DHFR
REACTOME: DHFR
ConsensusPathDB
Pathway Commons: DHFR
MetabolismMetaCyc: DHFR
HUMANCyc: DHFR
RegulationEnsembl's Regulation: ENSG00000228716
miRBase: chr5 :79,922,044-79,950,800
TargetScan: NM_000791
cisRED: ENSG00000228716
ContextiHOP: DHFR
cancer metabolism search in PubMed: DHFR
UCL Cancer Institute: DHFR
Assigned class in ccmGDBC

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

Mutations for DHFR
* 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 DHFR related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
M33552DHFR14657994633579946450LSP14116311118743071913492
BC068072ZMIZ111267108107071181073434DHFR1262131557994766979947722
DB727835DHFR26657994760079947664TM9SF362675109832177598346664
DA541950DHFR110757994731879947424PSMD21085563184019408184020492
L42531GSS11690203351640533543560DHFR1691181157994669579946815
AK123238ZNF483222949114309598114311891DHFR2285236657994678579946866
BQ328186DHFR18125957994584179945919SPPL325058612121222150121229364

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)                 
LOSS (# sample)   1  1          
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=11)		Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr5:79945224-79945224p.L76I2
chr5:79945254-79945254p.R66*2
chr5:79924930-79924930p.F180F1
chr5:79945268-79945268p.I61T1
chr5:79924953-79924953p.E173K1
chr5:79949865-79949865p.R33T1
chr5:79924971-79924971p.L167I1
chr5:79924972-79924972p.V166V1
chr5:79933712-79933712p.S120Y1
chr5:79933735-79933735p.M112I1

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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
# sample   1  3 1  1       4
# mutation   1  3 1  1       5
nonsynonymous SNV   1  3 1  1       4
synonymous SNV                   1
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
chr5:79945224p.L24I,DHFR2
chr5:79924930p.F128F,DHFR1
chr5:79924954p.E120D,DHFR1
chr5:79924971p.L115I,DHFR1
chr5:79924972p.S128A1
chr5:79929781p.L82I,DHFR1
chr5:79929790p.H79Y,DHFR1
chr5:79933712p.S68Y,DHFR1
chr5:79933760p.P52Q,DHFR1
chr5:79945217p.R26K,DHFR1

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 DHFR 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 DHFR

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

ANKRD32,BUB1B,CASC5,CCNB1,CDC25C,CENPK,DHFR,
FANCI,HMMR,KIF11,KNTC1,LMNB1,NUSAP1,PRIM1,
RACGAP1,RRM1,SMC2,TIMELESS,TMEM194A,WDR76,ZNF367		CLMP,ASPH,DDHD2,DHFR,DMGDH,EBF1,EHBP1,
RMDN1,FERMT2,GLYAT,KCTD20,LAMA4,MMD,MRAS,
PALM2-AKAP2,RHOBTB3,SEPT11,SLC25A16,SORBS1,TSPAN3,VKORC1L1

ASF1B,CCNA2,CCNB1,CDC45,CDK1,CENPK,CENPM,
CENPN,DEPDC1B,DHFR,H2AFZ,HMMR,KIAA0101,OIP5,
POC1A,POLA2,PRIM1,RAD51,UBE2T,WDR76,ZWINT		ASF1B,CDK1,DHFR,DNAJC9,ESCO2,KIAA0101,KIAA1524,
MAD2L1,ORC6,PCNA,POLA2,RAD51,RAD51AP1,RAD54B,
RFC3,RFC5,SGOL1,SPC25,TFDP1,VRK1,ZWILCH
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 DHFR
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
DB00157dihydrofolate reductaseapproved; nutraceuticalNADH
DB00205dihydrofolate reductaseapprovedPyrimethamine
DB00440dihydrofolate reductaseapprovedTrimethoprim
DB00563dihydrofolate reductaseapprovedMethotrexate
DB00642dihydrofolate reductaseapproved; investigationalPemetrexed
DB01131dihydrofolate reductaseapprovedProguanil
DB01157dihydrofolate reductaseapprovedTrimetrexate
DB02104dihydrofolate reductaseexperimental2,4-Diamino-5-Methyl-6-[(3,4,5-Trimethoxy-N-Methylanilino)Methyl]Pyrido[2,3-D]Pyrimidine
DB02427dihydrofolate reductaseexperimental2,4-Diamino-6-[N-(2',5'-Dimethoxybenzyl)-N-Methylamino]Quinazoline
DB02559dihydrofolate reductaseexperimental6-(Octahydro-1h-Indol-1-Ylmethyl)Decahydroquinazoline-2,4-Diamine
DB02583dihydrofolate reductaseexperimentalN6-(2,5-Dimethoxy-Benzyl)-N6-Methyl-Pyrido[2,3-D]Pyrimidine-2,4,6-Triamine
DB02919dihydrofolate reductaseexperimental2,4-Diamino-6-[N-(3',4',5'-Trimethoxybenzyl)-N-Methylamino]Pyrido[2,3-D]Pyrimidine
DB03060dihydrofolate reductaseexperimentalSri-9662
DB03125dihydrofolate reductaseexperimental2,4-Diamino-5-(3,4,5-Trimethoxy-Benzyl)-Pyrimidin-1-Ium
DB03351dihydrofolate reductaseexperimentalSri-9439
DB03461dihydrofolate reductaseexperimental2'-Monophosphoadenosine 5'-Diphosphoribose
DB03695dihydrofolate reductaseexperimental6-(2,5-Dimethoxy-Benzyl)-5-Methyl-Pyrido[2,3-D]Pyrimidine-2,4-Diamine
DB03886dihydrofolate reductaseexperimentalBiopterin
DB03987dihydrofolate reductaseexperimental2,4-Diamino-6-[N-(3',5'-Dimethoxybenzyl)-N-Methylamino]Pyrido[2,3-D]Pyrimidine
DB07140dihydrofolate reductaseexperimental5-[(3R)-3-(5-methoxybiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
DB07141dihydrofolate reductaseexperimental5-[(3R)-3-(5-methoxy-4'-methylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
DB07142dihydrofolate reductaseexperimental5-[(3R)-3-(5-methoxy-3',5'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
DB07144dihydrofolate reductaseexperimental5-[(3R)-3-(5-methoxy-2',6'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
DB08234dihydrofolate reductaseexperimental5-[3-(2,5-dimethoxyphenyl)prop-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine
DB08406dihydrofolate reductaseexperimental[N-(2,4-DIAMINOPTERIDIN-6-YL)-METHYL]-DIBENZ[B,F]AZEPINE
DB08448dihydrofolate reductaseexperimental(4aS)-5-[(2,4-diaminopteridin-6-yl)methyl]-4a,5-dihydro-2H-dibenzo[b,f]azepin-8-ol
DB08642dihydrofolate reductaseexperimental(2R,6S)-6-{[methyl(3,4,5-trimethoxyphenyl)amino]methyl}-1,2,5,6,7,8-hexahydroquinazoline-2,4-diamine
DB01929dihydrofolate reductaseexperimental5-Chloryl-2,4,6-Quinazolinetriamine
DB01958dihydrofolate reductaseexperimental5-[4-Tert-Butylphenylsulfanyl]-2,4-Quinazolinediamine
DB02001dihydrofolate reductaseexperimental5-(4-Morpholin-4-Yl-Phenylsulfanyl)-2,4-Quinazolinediamine
DB02402dihydrofolate reductaseexperimental5-(4-Methoxyphenoxy)-2,4-Quinazolinediamine
DB03814dihydrofolate reductaseexperimental2-(N-Morpholino)-Ethanesulfonic Acid
DB04163dihydrofolate reductaseexperimental5-Phenylsulfanyl-2,4-Quinazolinediamine
DB04306dihydrofolate reductaseexperimental5-[(4-Methylphenyl)Sulfanyl]-2,4-Quinazolinediamine
DB02026dihydrofolate reductaseexperimentalFuro[2,3d]Pyrimidine Antifolate
DB02809dihydrofolate reductaseexperimentalBrodimoprim-4,6-Dicarboxylate
DB04007dihydrofolate reductaseexperimentalBromo-WR99210
DB02015dihydrofolate reductaseexperimentalDihydrofolic Acid
DB02363dihydrofolate reductaseexperimental2'-Monophosphoadenosine-5'-Diphosphate
DB02718dihydrofolate reductaseexperimental5-Formyl-6-Hydrofolic Acid
DB03625dihydrofolate reductaseexperimental5,10-Dideazatetrahydrofolic Acid
DB03904dihydrofolate reductaseexperimentalUrea
DB07262dihydrofolate reductaseexperimental1-{[N-(1-IMINO-GUANIDINO-METHYL)]SULFANYLMETHYL}-3-TRIFLUOROMETHYL-BENZENE
DB07938dihydrofolate reductaseexperimental5-[[(2R)-2-cyclopropyl-7,8-dimethoxy-chroman-5-yl]methyl]pyrimidine-2,4-diamine
DB08741dihydrofolate reductaseexperimental5-[[(2R)-2-cyclopropyl-7,8-dimethoxy-2H-chromen-5-yl]methyl]pyrimidine-2,4-diamine
DB00515dihydrofolate reductaseapprovedCisplatin
DB00531dihydrofolate reductaseapproved; investigationalCyclophosphamide
DB00970dihydrofolate reductaseapprovedDactinomycin
DB00997dihydrofolate reductaseapproved; investigationalDoxorubicin
DB00541dihydrofolate reductaseapproved; investigationalVincristine
DB00145dihydrofolate reductaseapproved; nutraceuticalGlycine
DB00133dihydrofolate reductaseapproved; nutraceuticalL-Serine
DB00158dihydrofolate reductaseapproved; nutraceuticalFolic Acid
DB00544dihydrofolate reductaseapprovedFluorouracil
DB01050dihydrofolate reductaseapprovedIbuprofen


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Cross referenced IDs for DHFR
* 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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