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 FDPS
Basic gene info.Gene symbolFDPS
Gene namefarnesyl diphosphate synthase
SynonymsFPPS|FPS
CytomapUCSC genome browser: 1q22
Genomic locationchr1 :155278538-155290457
Type of geneprotein-coding
RefGenesNM_001135821.1,
NM_001135822.1,NM_001242824.1,NM_001242825.1,NM_002004.3,
Ensembl idENSG00000160752
Description(2E,6E)-farnesyl diphosphate synthaseFPP synthaseFPP synthetasedimethylallyltranstransferasefarnesyl pyrophosphate synthasefarnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferasegeranyltranstransferase
Modification date20141207
dbXrefs MIM : 134629
HGNC : HGNC
Ensembl : ENSG00000160752
HPRD : 00606
Vega : OTTHUMG00000013909
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FDPS
BioGPS: 2224
Gene Expression Atlas: ENSG00000160752
The Human Protein Atlas: ENSG00000160752
PathwayNCI Pathway Interaction Database: FDPS
KEGG: FDPS
REACTOME: FDPS
ConsensusPathDB
Pathway Commons: FDPS
MetabolismMetaCyc: FDPS
HUMANCyc: FDPS
RegulationEnsembl's Regulation: ENSG00000160752
miRBase: chr1 :155,278,538-155,290,457
TargetScan: NM_001135821
cisRED: ENSG00000160752
ContextiHOP: FDPS
cancer metabolism search in PubMed: FDPS
UCL Cancer Institute: FDPS
Assigned class in ccmGDBC

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

Mutations for FDPS
* 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
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastFDPSchr1155286796155287196ASH1Lchr1155306027155306427
ovaryFDPSchr1155288695155288715DCST2chr1154991943154991963
pancreasFDPSchr1155279838155279858chr21613174916131769
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 FDPS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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=34)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=0)
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
chr1:155287783-155287783p.R178C2
chr1:155287966-155287966p.V190M2
chr1:155288068-155288068p.E224K2
chr1:155289467-155289467p.F304L2
chr1:155279651-155279651p.E24V2
chr1:155289628-155289628p.K323T1
chr1:155279946-155279946p.D97H1
chr1:155290326-155290326p.E396K1
chr1:155288489-155288489p.D240Y1
chr1:155279652-155279652p.E24D1

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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 3172 2 2  61   38 7
# mutation 3172 2 2  61   38 8
nonsynonymous SNV 1162 2 1  31   38 7
synonymous SNV 2 2    1  3       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
chr1:155288068p.E53K,FDPS2
chr1:155282164p.G89G,FDPS1
chr1:155288469p.G151R,FDPS1
chr1:155290306p.E24D,FDPS1
chr1:155279870p.V101V,FDPS1
chr1:155282171p.K152T,FDPS1
chr1:155288489p.Q52Q,FDPS1
chr1:155290326p.D2A,FDPS1
chr1:155279920p.N160K,FDPS1
chr1:155287752p.E56K,FDPS1

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 FDPS 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 FDPS

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

ACAT2,ADAM15,CKS1B,DAP3,EBP,FDPS,FLAD1,
HAX1,HDGF,JTB,MFSD2B,MVD,NDUFS2,PRCC,
SLC50A1,RUSC1,MSMO1,SCAMP3,TAGLN2,UBE2Q1,ZFP57
AACS,ACAT2,AKR1A1,DBI,DHCR7,EBP,FDPS,
FIBCD1,G6PD,GGT1,GGTLC2,GSS,HIST1H3D,MFSD7,
MMAB,MVD,MVK,NUDT8,P4HB,PEX10,QPRT

ACAT2,BPNT1,CYP51A1,DHCR24,ENSA,FDPS,FGFBP1,
FH,HSD17B7,IDI1,LGTN,LSS,MTX1,MVD,
NDUFS2,RAB25,MSMO1,SDHC,TIMM17A,TPM3,UQCRFS1
ACAT2,BATF3,C14orf1,C6orf223,EBP,FDFT1,FDPS,
HSD17B7,IDI1,INSIG1,MMAB,MVD,MVK,NSDHL,
PLA2G2A,PLA2G3,PSMA3,RDH11,MSMO1,SC5D,STARD4
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 FDPS
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
DB00282farnesyl diphosphate synthaseapprovedPamidronate
DB00399farnesyl diphosphate synthaseapprovedZoledronate
DB00630farnesyl diphosphate synthaseapprovedAlendronate
DB00710farnesyl diphosphate synthaseapproved; investigationalIbandronate
DB00884farnesyl diphosphate synthaseapproved; investigationalRisedronate
DB01785farnesyl diphosphate synthaseexperimentalDimethylallyl Diphosphate
DB02508farnesyl diphosphate synthaseexperimentalIsopentyl Pyrophosphate
DB02552farnesyl diphosphate synthaseexperimentalGeranyl Diphosphate
DB04714farnesyl diphosphate synthaseexperimentalISOPENTENYL PYROPHOSPHATE
DB07780farnesyl diphosphate synthaseexperimentalFARNESYL DIPHOSPHATE
DB07841farnesyl diphosphate synthaseexperimentalGERANYLGERANYL DIPHOSPHATE
DB00481farnesyl diphosphate synthaseapproved; investigationalRaloxifene


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Cross referenced IDs for FDPS
* 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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