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

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 FAR1

Basic gene info.	Gene symbol	FAR1
	Gene name	fatty acyl CoA reductase 1
	Synonyms	MLSTD2\|SDR10E1
	Cytomap	UCSC genome browser: 11p15.2
	Genomic location	chr11 :13690205-13753893
	Type of gene	protein-coding
	RefGenes	NM_032228.5,
	Ensembl id	ENSG00000197601
	Description	fatty acyl-CoA reductase 1male sterility domain containing 2male sterility domain-containing protein 2putative fatty acyl reductaseshort chain dehydrogenase/reductase family 10E, member 1
	Modification date	20141207
dbXrefs	MIM : 616107
	HGNC : HGNC
	Ensembl : ENSG00000197601
	HPRD : 14724
	Vega : OTTHUMG00000165743
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FAR1
	BioGPS: 84188
	Gene Expression Atlas: ENSG00000197601
	The Human Protein Atlas: ENSG00000197601
Pathway	NCI Pathway Interaction Database: FAR1
	KEGG: FAR1
	REACTOME: FAR1
	ConsensusPathDB
	Pathway Commons: FAR1
Metabolism	MetaCyc: FAR1
	HUMANCyc: FAR1
Regulation	Ensembl's Regulation: ENSG00000197601
	miRBase: chr11 :13,690,205-13,753,893
	TargetScan: NM_032228
	cisRED: ENSG00000197601
Context	iHOP: FAR1
	cancer metabolism search in PubMed: FAR1
	UCL Cancer Institute: FAR1
Assigned class in ccmGDB	C

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Phenotypic Information for FAR1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: FAR1
	Familial Cancer Database: FAR1

* 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_PEROXISOMAL_LIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: FAR1
	MedGen: FAR1 (Human Medical Genetics with Condition)
	ClinVar: FAR1
Phenotype	MGI: FAR1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: FAR1

Mutations for FAR1

* 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

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- 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
ovary	FAR1	chr11	13697092	13697112	FAR1	chr11	13697303	13697323
ovary	FAR1	chr11	13746361	13746381	FAR1	chr11	13751598	13751618
pancreas	FAR1	chr11	13699927	13699947	SPON1	chr11	14119415	14119435
pancreas	FAR1	chr11	13699927	13699947	SPON1	chr11	14119417	14119437

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 FAR1 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
BE707585	PHKB	1	136	16	47733251	47733387	FAR1	128	292	11	13749157	13750249
AA862191	FAR1	9	75	11	13694560	13694626	FAR1	64	212	11	13694423	13694571
DA215427	CTNNB1	3	173	3	41240992	41241162	FAR1	171	538	11	13743275	13750266
BF906017	FAR1	1	97	11	13695482	13695580	FAR1	92	408	11	13692089	13692402
BI019366	FAR1	1	99	11	13695482	13695580	FAR1	94	360	11	13692089	13692352
BI019383	FAR1	1	99	11	13695482	13695580	FAR1	94	442	11	13692089	13692434

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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)

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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=2)
There's no deleted snv.

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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
chr11:13733493-13733493	p.R263*	3
chr11:13729529-13729529	p.H150Y	2
chr11:13721922-13721922	p.N83S	2
chr11:13729478-13729478	p.R133*	2
chr11:13749178-13749178	p.V445I	1
chr11:13732384-13732384	p.S230S	1
chr11:13733566-13733566	p.A287V	1
chr11:13721879-13721880	p.R69fs*14	1
chr11:13736181-13736181	p.A361T	1
chr11:13729486-13729486	p.L135L	1

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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	1		3			3		2			4	2	1			3	6		6
# mutation	3	1		3			3		2			4	2	1			4	6		6
nonsynonymous SNV	2			2			3		1			3	1	1			2	3		5
synonymous SNV	1	1		1					1			1	1				2	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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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
chr11:13749116	p.V425I	1
chr11:13729544	p.W236L	1
chr11:13734540	p.A431A	1
chr11:13749118	p.G242A	1
chr11:13729621	p.Y444Y	1
chr11:13734550	p.M1I	1
chr11:13749138	p.A287V	1
chr11:13732282	p.V445I	1
chr11:13736088	p.V42F	1
chr11:13716315	p.P297P	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 FAR1 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 FAR1

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))

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CNV 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

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


ALG10B,AP1AR,BTBD10,C11orf58,COPB1,CTR9,DMXL1, DPY19L4,FAR1,GAB1,IPO7,LARP4,LIN7C,LRBA, METTL15,MFSD8,PIK3C2A,SPTY2D1,UEVLD,USP38,USP47	ACAP2,C16orf52,C5orf24,CDK17,CHIC1,DPY19L4,FAM91A1, FAR1,FMR1,GABPA,LYSMD3,MIER1,MTMR6,PRKAA1, SOCS4,STAM2,TMED7,TMEM106B,TMEM168,TMEM30A,TROVE2

ANKRD28,API5,CENPE,CKAP5,DLAT,DLGAP5,E2F8, FANCM,FAR1,GNPNAT1,KIF18A,NEDD1,PDE12,PDHX, RRM1,SAAL1,SASS6,SRSF1,SGOL1,SMC4,TMEM41B	BRCC3,CAAP1,DTWD2,FAM76B,FAM91A1,FAR1,FASTKD1, LARP4,MECOM,NIPAL2,PDE12,PPIP5K2,PRPF40A,PRPF4B, SLC30A9,SMC5,SOCS4,TDG,TMEM167A,TMEM168,ZNF562

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

: Open all plots for all cancer types

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Interacting 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 FAR1

There's no related Drug.

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Cross referenced IDs for FAR1

* 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