Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 RFT1
Basic gene info.Gene symbolRFT1
Gene nameRFT1 homolog (S. cerevisiae)
SynonymsCDG1N
CytomapUCSC genome browser: 3p21.1
Genomic locationchr3 :53122500-53164470
Type of geneprotein-coding
RefGenesNM_052859.3,
Ensembl idENSG00000163933
DescriptionRFT1, requiring fifty three 1 homologcongenital disorder of glycosylation 1Nprotein RFT1 homologputative endoplasmic reticulum multispan transmembrane protein
Modification date20141219
dbXrefs MIM : 611908
HGNC : HGNC
Ensembl : ENSG00000163933
HPRD : 15239
Vega : OTTHUMG00000074035
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RFT1
BioGPS: 91869
Gene Expression Atlas: ENSG00000163933
The Human Protein Atlas: ENSG00000163933
PathwayNCI Pathway Interaction Database: RFT1
KEGG: RFT1
REACTOME: RFT1
ConsensusPathDB
Pathway Commons: RFT1
MetabolismMetaCyc: RFT1
HUMANCyc: RFT1
RegulationEnsembl's Regulation: ENSG00000163933
miRBase: chr3 :53,122,500-53,164,470
TargetScan: NM_052859
cisRED: ENSG00000163933
ContextiHOP: RFT1
cancer metabolism search in PubMed: RFT1
UCL Cancer Institute: RFT1
Assigned class in ccmGDBC

Top
Phenotypic Information for RFT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RFT1
Familial Cancer Database: RFT1
* 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_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: RFT1
MedGen: RFT1 (Human Medical Genetics with Condition)
ClinVar: RFT1
PhenotypeMGI: RFT1 (International Mouse Phenotyping Consortium)
PhenomicDB: RFT1

Mutations for RFT1
* 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 RFT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW376337MAPK1176222211698922117064RFT16722135312658653133502
AW376334MAPK14147222211698922117132RFT113829235312658653133502
AW752527MAPK1170222211699422117063RFT16622035312658653133502

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
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)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr3:53159945-53159945p.I43I4
chr3:53139708-53139708p.D313V2
chr3:53126460-53126460p.P461P1
chr3:53156398-53156398p.K150*1
chr3:53138079-53138079p.S331F1
chr3:53159972-53159972p.F34F1
chr3:53145912-53145912p.W237G1
chr3:53126463-53126463p.R460R1
chr3:53156419-53156419p.A143T1
chr3:53138093-53138094p.A326fs*381

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  5  2 1  5 1  75 8
# mutation2  5  2 1  6 1  75 8
nonsynonymous SNV   3  1 1  2 1  25 5
synonymous SNV2  2  1    4    5  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])

Top
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
chr3:53159945p.I43I3
chr3:53126559p.D402N1
chr3:53145912p.S164S1
chr3:53156537p.A394S1
chr3:53126615p.M147V1
chr3:53153907p.G359G1
chr3:53157753p.W140L1
chr3:53133401p.A354A1
chr3:53153929p.A130V1
chr3:53157763p.D313D1

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 RFT1 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]

Top
Gene Expression for RFT1

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ABHD14B,ACY1,BAP1,ELP6,CCDC51,EXOSC7,GNL3,
IFRD2,MAPKAPK3,NCKIPSD,NPRL2,PSMD6,RFT1,RRP9,
SPCS1,TEX264,THOC7,TKT,TMEM42,TUSC2,UQCRC1
ASNS,SAYSD1,CDCA7L,CEACAM1,CNOT10,CTNNB1,MCTP2,
NCOA5,PRPF38A,QTRTD1,RFC5,RFT1,SDR42E1,SMARCD1,
TDP1,TGIF2,TMEM87A,TP53,TRAF3IP2,CEP41,VGLL4

APEH,CCDC51,CDC25A,EXOSC7,GNL3,HEMK1,IFRD2,
KIF9,MAPKAPK3,NME1,NME6,RANBP1,RFT1,RPUSD3,
RRP9,RUVBL1,SPCS1,TEX264,TKT,TRAIP,TUSC2
AAAS,ALG1,ALG3,ALG8,ATIC,SAPCD2,DPAGT1,
FBL,HMGA1,HNRNPA1L2,IMPDH2,MESDC2,METTL13,MRPL37,
PAICS,RFT1,SHMT2,SSRP1,NELFCD,TRAP1,WDR46
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for RFT1


There's no related Drug.
Top
Cross referenced IDs for RFT1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas