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 RFK
Basic gene info.Gene symbolRFK
Gene nameriboflavin kinase
SynonymsRIFK
CytomapUCSC genome browser: 9q21.13
Genomic locationchr9 :79000432-79009444
Type of geneprotein-coding
RefGenesNM_018339.5,
Ensembl idENSG00000135002
Description0610038L10RikATP:riboflavin 5'-phosphotransferaseflavokinase
Modification date20141207
dbXrefs MIM : 613010
HGNC : HGNC
Ensembl : ENSG00000135002
HPRD : 17969
Vega : OTTHUMG00000020040
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RFK
BioGPS: 55312
Gene Expression Atlas: ENSG00000135002
The Human Protein Atlas: ENSG00000135002
PathwayNCI Pathway Interaction Database: RFK
KEGG: RFK
REACTOME: RFK
ConsensusPathDB
Pathway Commons: RFK
MetabolismMetaCyc: RFK
HUMANCyc: RFK
RegulationEnsembl's Regulation: ENSG00000135002
miRBase: chr9 :79,000,432-79,009,444
TargetScan: NM_018339
cisRED: ENSG00000135002
ContextiHOP: RFK
cancer metabolism search in PubMed: RFK
UCL Cancer Institute: RFK
Assigned class in ccmGDBC

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

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

Mutations for RFK
* 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 RFK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC015473RFK1104697900191679009266LYZ10471534126974752769748014
Z25253SGCD2685155771567155771633RFK5826197900072479000926

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=11)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=1)

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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
chr9:79002369-79002369p.I145M3
chr9:79007414-79007415p.S59fs*82
chr9:79009015-79009015p.I32V1
chr9:79002415-79002415p.I130T1
chr9:79009074-79009074p.P12L1
chr9:79002418-79002418p.D129V1
chr9:79002428-79002428p.I126F1
chr9:79002433-79002433p.S124L1
chr9:79002440-79002440p.L122F1
chr9:79003486-79003486p.K114N1

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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
# sample11 1           1 1 1
# mutation11 1           1 1 1
nonsynonymous SNV11 1           1 1 1
synonymous SNV                    
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
chr9:79002418p.K107N1
chr9:79003486p.V100A1
chr9:79003508p.I25V1
chr9:79009015p.D141N1
chr9:79002362p.I123T1
chr9:79002415p.D122V1

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 RFK 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 RFK

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

BSPH1,C2orf69,LINC00588,C9orf41,ISCA1,ISCA1P1,LEUTX,
PRAMEF5,PRAMEF9,RAB14,RBM18,RFK,RFPL4B,PTBP3,
SCAMP1,SIM1,SPRR3,SPTLC1,TPRX1,TRIM53AP,UBQLN1
ABHD13,TMEM263,MZT1,C1D,CHMP2B,COMMD8,EIF4E,
FAM3C,IMPA1,MOB4,MOSPD1,RFK,SELT,SMNDC1,
SPCS3,TRAM1,TXNDC9,UBE2D3,UBE2E1,UBLCP1,ZCCHC10

ARL5A,ATP6V1G1,C12orf29,C1D,TRAPPC13,COMMD8,ISCA1,
ISCA1P1,MOB4,PDCD10,RARS2,RFK,RNASEH2B,RSL24D1,
SLC35D2,SPTLC1,SRP9,TGDS,TXNDC9,YWHAQ,ZCCHC10
ARPC5,ABRACL,CASP7,CHMP2B,GDPD3,GHITM,GNG12,
GRAMD3,HPGD,LRRC19,MIER1,MYL12B,NAT1,SLC51B,
RAC1,RFK,SPPL2A,SRI,TPMT,UBE2A,WSB2
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 RFK
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
DB00140riboflavin kinaseapproved; nutraceuticalRiboflavin
DB03247riboflavin kinaseexperimentalRiboflavin Monophosphate
DB03431riboflavin kinaseexperimentalAdenosine-5'-Diphosphate


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Cross referenced IDs for RFK
* 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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