Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	FDPS
	Gene name	farnesyl diphosphate synthase
	Synonyms	FPPS\|FPS
	Cytomap	UCSC genome browser: 1q22
	Genomic location	chr1 :155278538-155290457
	Type of gene	protein-coding
	RefGenes	NM_001135821.1, NM_001135822.1,NM_001242824.1,NM_001242825.1,NM_002004.3,
	Ensembl id	ENSG00000160752
	Description	(2E,6E)-farnesyl diphosphate synthaseFPP synthaseFPP synthetasedimethylallyltranstransferasefarnesyl pyrophosphate synthasefarnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferasegeranyltranstransferase
	Modification date	20141207
dbXrefs	MIM : 134629
	HGNC : HGNC
	Ensembl : ENSG00000160752
	HPRD : 00606
	Vega : OTTHUMG00000013909
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FDPS
	BioGPS: 2224
	Gene Expression Atlas: ENSG00000160752
	The Human Protein Atlas: ENSG00000160752
Pathway	NCI Pathway Interaction Database: FDPS
	KEGG: FDPS
	REACTOME: FDPS
	ConsensusPathDB
	Pathway Commons: FDPS
Metabolism	MetaCyc: FDPS
	HUMANCyc: FDPS
Regulation	Ensembl's Regulation: ENSG00000160752
	miRBase: chr1 :155,278,538-155,290,457
	TargetScan: NM_001135821
	cisRED: ENSG00000160752
Context	iHOP: FDPS
	cancer metabolism search in PubMed: FDPS
	UCL Cancer Institute: FDPS
Assigned class in ccmGDB	C

Top

Phenotypic Information for FDPS(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: FDPS
	MedGen: FDPS (Human Medical Genetics with Condition)
	ClinVar: FDPS
Phenotype	MGI: FDPS (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	FDPS	chr1	155286796	155287196	ASH1L	chr1	155306027	155306427
ovary	FDPS	chr1	155288695	155288715	DCST2	chr1	154991943	154991963
pancreas	FDPS	chr1	155279838	155279858		chr2	16131749	16131769

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows FDPS related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BG491331	PMM2	2	666	16	8891714	8906963	FDPS	667	899	1	155287732	155288485
BM809442	PMM2	1	664	16	8891715	8906963	FDPS	665	965	1	155287732	155288655
BF512311	FDPS	18	159	1	155290315	155290456	ATP13A2	151	446	1	17316435	17318299
CB046420	GPI	24	326	19	34868441	34870455	FDPS	322	436	1	155290342	155290456
BM555536	PMM2	1	665	16	8891714	8906963	FDPS	666	970	1	155287732	155288545
CA312317	VPS52	1	138	6	4708320	4708717	FDPS	133	762	1	155284139	155285195
CB046419	FDPS	35	149	1	155290342	155290456	GPI	145	447	19	34868441	34870455
BF928396	FDPS	16	216	1	155289617	155290297	TGIF2	207	416	20	35215649	35215858

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

Top

SNV 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

Top

Somatic 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.

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr1:155279651-155279651	p.E24V	2
chr1:155287783-155287783	p.R178C	2
chr1:155287966-155287966	p.V190M	2
chr1:155288068-155288068	p.E224K	2
chr1:155289467-155289467	p.F304L	2
chr1:155287769-155287769	p.D173A	1
chr1:155290322-155290322	p.L394L	1
chr1:155288469-155288469	p.T233S	1
chr1:155279946-155279946	p.D97H	1
chr1:155289628-155289628	p.K323T	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		3	1	7	2		2		2			6	1				3	8		7
# mutation		3	1	7	2		2		2			6	1				3	8		8
nonsynonymous SNV		1	1	6	2		2		1			3	1				3	8		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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr1:155288068	p.E53K,FDPS	2
chr1:155279838	p.Q5H,FDPS	1
chr1:155290280	p.V19M,FDPS	1
chr1:155282164	p.S218N,FDPS	1
chr1:155288469	p.S22F,FDPS	1
chr1:155279870	p.D26G,FDPS	1
chr1:155290306	p.E225K,FDPS	1
chr1:155282171	p.E30K,FDPS	1
chr1:155288489	p.L40L,FDPS	1
chr1:155279920	p.V235I,FDPS	1

Other 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

Copy 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]

Top

Gene Expression for FDPS

Gene 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.

Differential 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

CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

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

Top

Pharmacological Information for FDPS

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00282	farnesyl diphosphate synthase	approved	Pamidronate
DB00399	farnesyl diphosphate synthase	approved	Zoledronate
DB00630	farnesyl diphosphate synthase	approved	Alendronate
DB00710	farnesyl diphosphate synthase	approved; investigational	Ibandronate
DB00884	farnesyl diphosphate synthase	approved; investigational	Risedronate
DB01785	farnesyl diphosphate synthase	experimental	Dimethylallyl Diphosphate
DB02508	farnesyl diphosphate synthase	experimental	Isopentyl Pyrophosphate
DB02552	farnesyl diphosphate synthase	experimental	Geranyl Diphosphate
DB04714	farnesyl diphosphate synthase	experimental	ISOPENTENYL PYROPHOSPHATE
DB07780	farnesyl diphosphate synthase	experimental	FARNESYL DIPHOSPHATE
DB07841	farnesyl diphosphate synthase	experimental	GERANYLGERANYL DIPHOSPHATE
DB00481	farnesyl diphosphate synthase	approved; investigational	Raloxifene

Top

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