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 FDFT1

Basic gene info.	Gene symbol	FDFT1
	Gene name	farnesyl-diphosphate farnesyltransferase 1
	Synonyms	DGPT\|ERG9\|SQS\|SS
	Cytomap	UCSC genome browser: 8p23.1-p22
	Genomic location	chr8 :11660189-11696818
	Type of gene	protein-coding
	RefGenes	NM_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 id	ENSG00000079459
	Description	FPP:FPP farnesyltransferasepresqualene-di-diphosphate synthasesqualene synthasesqualene synthetase
	Modification date	20141207
dbXrefs	MIM : 184420
	HGNC : HGNC
	Ensembl : ENSG00000079459
	HPRD : 01694
	Vega : OTTHUMG00000090801
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FDFT1
	BioGPS: 2222
	Gene Expression Atlas: ENSG00000079459
	The Human Protein Atlas: ENSG00000079459
Pathway	NCI Pathway Interaction Database: FDFT1
	KEGG: FDFT1
	REACTOME: FDFT1
	ConsensusPathDB
	Pathway Commons: FDFT1
Metabolism	MetaCyc: FDFT1
	HUMANCyc: FDFT1
Regulation	Ensembl's Regulation: ENSG00000079459
	miRBase: chr8 :11,660,189-11,696,818
	TargetScan: NM_001287742
	cisRED: ENSG00000079459
Context	iHOP: FDFT1
	cancer metabolism search in PubMed: FDFT1
	UCL Cancer Institute: FDFT1
Assigned class in ccmGDB	C

Top

Phenotypic Information for FDFT1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: FDFT1
	MedGen: FDFT1 (Human Medical Genetics with Condition)
	ClinVar: FDFT1
Phenotype	MGI: FDFT1 (International Mouse Phenotyping Consortium)
Phenotype	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.

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

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows FDFT1 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
N34721	PCMTD1	1	69	8	52811489	52811558	FDFT1	54	311	8	11666293	11667320
BF996032	FDFT1	7	479	8	11684537	11685009	ARHGAP31	471	590	3	119045546	119045665

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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

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=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.

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
chr8:11667179-11667179	p.N67N	3
chr8:11679263-11679263	p.S129Y	2
chr8:11666348-11666348	p.Q49E	2
chr8:11679307-11679307	p.A144T	2
chr8:11683599-11683599	p.E193K	2
chr8:11667360-11667360	p.?	1
chr8:11683691-11683691	p.D223D	1
chr8:11666332-11666332	p.C43C	1
chr8:11695919-11695919	p.S352L	1
chr8:11683712-11683712	p.F230L	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		1		4			4		1			3	1			1	1	1		2
# mutation		1		4			4		1			3	1			1	1	1		2
nonsynonymous SNV		1		4			3		1			2	1							2
synonymous SNV							1					1				1	1	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
chr8:11683712	p.V149V,FDFT1	1
chr8:11667248	p.T201M,FDFT1	1
chr8:11687765	p.F184F,FDFT1	1
chr8:11667353	p.S221L,FDFT1	1
chr8:11687842	p.P185Q,FDFT1	1
chr8:11667355	p.D204N,FDFT1	1
chr8:11687890	p.R207Q,FDFT1	1
chr8:11679310	p.R208I,FDFT1	1
chr8:11689122	p.Y233C,FDFT1	1
chr8:11679320	p.R244H,FDFT1	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 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]

Top

Gene Expression for FDFT1

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


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

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 FDFT1

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
DB00630	farnesyl-diphosphate farnesyltransferase 1	approved	Alendronate
DB00710	farnesyl-diphosphate farnesyltransferase 1	approved; investigational	Ibandronate
DB00282	farnesyl-diphosphate farnesyltransferase 1	approved	Pamidronate
DB00884	farnesyl-diphosphate farnesyltransferase 1	approved; investigational	Risedronate
DB00399	farnesyl-diphosphate farnesyltransferase 1	approved	Zoledronate

Top

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