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 FDFT1
Basic gene info.Gene symbolFDFT1
Gene namefarnesyl-diphosphate farnesyltransferase 1
SynonymsDGPT|ERG9|SQS|SS
CytomapUCSC genome browser: 8p23.1-p22
Genomic locationchr8 :11660189-11696818
Type of geneprotein-coding
RefGenesNM_001287742.1,
NM_001287743.1,NM_001287744.1,NM_001287745.1,NM_001287747.1,
NM_001287748.1,NM_001287749.1,NM_001287750.1,NM_001287751.1,
NM_001287756.1,NM_004462.4,
Ensembl idENSG00000079459
DescriptionFPP:FPP farnesyltransferasepresqualene-di-diphosphate synthasesqualene synthasesqualene synthetase
Modification date20141207
dbXrefs MIM : 184420
HGNC : HGNC
Ensembl : ENSG00000079459
HPRD : 01694
Vega : OTTHUMG00000090801
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FDFT1
BioGPS: 2222
Gene Expression Atlas: ENSG00000079459
The Human Protein Atlas: ENSG00000079459
PathwayNCI Pathway Interaction Database: FDFT1
KEGG: FDFT1
REACTOME: FDFT1
ConsensusPathDB
Pathway Commons: FDFT1
MetabolismMetaCyc: FDFT1
HUMANCyc: FDFT1
RegulationEnsembl's Regulation: ENSG00000079459
miRBase: chr8 :11,660,189-11,696,818
TargetScan: NM_001287742
cisRED: ENSG00000079459
ContextiHOP: FDFT1
cancer metabolism search in PubMed: FDFT1
UCL Cancer Institute: FDFT1
Assigned class in ccmGDBC

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Phenotypic Information for FDFT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: FDFT1
Familial Cancer Database: FDFT1
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: FDFT1
MedGen: FDFT1 (Human Medical Genetics with Condition)
ClinVar: FDFT1
PhenotypeMGI: FDFT1 (International Mouse Phenotyping Consortium)
PhenomicDB: FDFT1

Mutations for FDFT1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows FDFT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
N34721PCMTD116985281148952811558FDFT15431181166629311667320
BF996032FDFT1747981168453711685009ARHGAP314715903119045546119045665

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              2  
GAIN (# sample)              2  
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=21)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr8:11667179-11667179p.N67N3
chr8:11683599-11683599p.E193K2
chr8:11679263-11679263p.S129Y2
chr8:11666348-11666348p.Q49E2
chr8:11679307-11679307p.A144T2
chr8:11683576-11683576p.R185H1
chr8:11689119-11689119p.L324L1
chr8:11667306-11667306p.R110W1
chr8:11689122-11689122p.M325I1
chr8:11660352-11660352p.V4A1

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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
# sample 1 4  4 1  31  111 2
# mutation 1 4  4 1  31  111 2
nonsynonymous SNV 1 4  3 1  21      2
synonymous SNV      1    1   111  
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
chr8:11683543p.D56D,FDFT11
chr8:11696027p.F63L,FDFT11
chr8:11683576p.Y72H,FDFT11
chr8:11683666p.T97T,FDFT11
chr8:11660408p.L113L,FDFT11
chr8:11683691p.M158I,FDFT11
chr8:11666366p.G18E,FDFT11
chr8:11683712p.P165T,FDFT11
chr8:11667248p.A114T,FDFT11
chr8:11687765p.T201M,FDFT11

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 FDFT1 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 FDFT1

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

AKR1B15,AKR1D1,C6orf223,CCDC25,EYS,FBXO25,FDFT1,
IDI1,INTS10,MCPH1,MTMR9,MYOM2,NEIL2,REEP4,
RLN3,RNASE11,RNASE12,SC5D,SPINK8,VPS37A,XPO7
AACS,ACSL3,ADAM2,ALOX15B,APOD,DHRS2,FDFT1,
G6PD,HIST1H4H,HPGD,IDI1,IVD,NANOG,PLA2G4E,
PNLIPRP3,PPEF1,SERHL2,SERHL,SULT1C3,UGT2B11,UGT2B28

AGPAT5,BIN3,CCDC25,CDCA2,CNOT7,DCTN6,ERI1,
ESCO2,FDFT1,GSR,INTS10,INTS9,KCTD9,CCAR2,
MCPH1,NAT1,PBK,PINX1,PPP2R2A,SH2D4A,VPS37A
ACAT2,C14orf1,C6orf223,CYP51A1,DHCR24,DHCR7,EBP,
FDFT1,FDPS,HMGCR,HMGCS1,IDI1,INSIG1,MVD,
MVK,NSDHL,PCSK9,PLA2G3,MSMO1,SC5D,SQLE
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 FDFT1
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
DB00630farnesyl-diphosphate farnesyltransferase 1approvedAlendronate
DB00710farnesyl-diphosphate farnesyltransferase 1approved; investigationalIbandronate
DB00282farnesyl-diphosphate farnesyltransferase 1approvedPamidronate
DB00884farnesyl-diphosphate farnesyltransferase 1approved; investigationalRisedronate
DB00399farnesyl-diphosphate farnesyltransferase 1approvedZoledronate


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Cross referenced IDs for FDFT1
* 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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