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 FAR2

Basic gene info.	Gene symbol	FAR2
	Gene name	fatty acyl CoA reductase 2
	Synonyms	MLSTD1\|SDR10E2
	Cytomap	UCSC genome browser: 12p11.22
	Genomic location	chr12 :29376597-29487006
	Type of gene	protein-coding
	RefGenes	NM_001271783.1, NM_001271784.1,NM_018099.4,
	Ensembl id	ENSG00000064763
	Description	fatty acyl-CoA reductase 2male sterility domain-containing protein 1short chain dehydrogenase/reductase family 10E, member 2
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000064763
	HPRD : 14723
	Vega : OTTHUMG00000169320
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FAR2
	BioGPS: 55711
	Gene Expression Atlas: ENSG00000064763
	The Human Protein Atlas: ENSG00000064763
Pathway	NCI Pathway Interaction Database: FAR2
	KEGG: FAR2
	REACTOME: FAR2
	ConsensusPathDB
	Pathway Commons: FAR2
Metabolism	MetaCyc: FAR2
	HUMANCyc: FAR2
Regulation	Ensembl's Regulation: ENSG00000064763
	miRBase: chr12 :29,376,597-29,487,006
	TargetScan: NM_001271783
	cisRED: ENSG00000064763
Context	iHOP: FAR2
	cancer metabolism search in PubMed: FAR2
	UCL Cancer Institute: FAR2
Assigned class in ccmGDB	C

Top

Phenotypic Information for FAR2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: FAR2
	Familial Cancer Database: FAR2

* 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: FAR2
	MedGen: FAR2 (Human Medical Genetics with Condition)
	ClinVar: FAR2
Phenotype	MGI: FAR2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: FAR2

Mutations for FAR2

* 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
pancreas	FAR2	chr12	29414159	29414179		chr15	35485999	35486019
pancreas	FAR2	chr12	29457071	29457091		chr12	30617190	30617210
pancreas	FAR2	chr12	29457071	29457091		chr12	30617199	30617219

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 FAR2 related fusion information.

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

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	1	1							3		2			1	1		1
GAIN (# sample)	1	1							3		2			1	1		1
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=41)	Stat. for Synonymous SNVs (# total SNVs=22)

Stat. for Deletions (# total SNVs=6)	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
chr12:29450110-29450110	p.I177fs*8	4
chr12:29423460-29423460	p.L26L	3
chr12:29485611-29485611	p.L446M	3
chr12:29446406-29446406	p.L121L	3
chr12:29474839-29474839	p.L413L	3
chr12:29462135-29462135	p.I247R	2
chr12:29450121-29450121	p.I178T	2
chr12:29474809-29474809	p.T403T	2
chr12:29423409-29423409	p.G9G	2
chr12:29450007-29450009	p.S140_Q141>K	2

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		2		6			1		1	1		12	4				4	7		10
# mutation		2		6			1		1	1		14	4				4	7		14
nonsynonymous SNV		1		5					1			7	1				4	6		9
synonymous SNV		1		1			1			1		7	3					1		5

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
chr12:29446285	p.I380I,FAR2	2
chr12:29423409	p.G9G,FAR2	2
chr12:29423429	p.T16M,FAR2	2
chr12:29486610	p.A81D,FAR2	2
chr12:29460611	p.N9H,FAR2	1
chr12:29464850	p.V184V,FAR2	1
chr12:29474843	p.N332S,FAR2	1
chr12:29460616	p.L24L,FAR2	1
chr12:29469849	p.A196S,FAR2	1
chr12:29446289	p.L334L,FAR2	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 FAR2 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 FAR2

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


ACER1,ACSBG1,AWAT1,AWAT2,C1orf105,CARD18,CYP2F1, CYP3A4,DGAT2,DGAT2L6,ELOVL4,ERGIC2,FA2H,FADS6, FAR2,KRT79,PLA2G2F,PNPLA1,PSAPL1,SOAT1,VSX2	ADAM2,ALOX15B,APOD,C15orf43,CTNNA2,DHRS2,ELOVL7, ENPP3,EPS8L3,FAR2,HIST1H2AG,HPGD,IDI1,IYD, LST-3TM12,NANOG,RNASE12,SCP2,SERHL,SULT1C3,TMPRSS11F

A1CF,ABCD3,AGMAT,ALDH2,CASP6,CMAS,FAR2, GGT6,GPA33,GUCY2C,HADH,HOOK1,KLHL8,MAOA, MAPKAPK5,PKP2,SLC35A3,SMAGP,SUCLG2,TMBIM6,TMED5	ATP8B1,BDH1,C12orf49,MCU,CD24,CKMT1B,CSTF2, DARS2,ESRP1,FAR2,FUT3,GJB2,GOLM1,GOT1, HNRNPAB,MTIF2,AP5M1,NARS,NSF,PGGT1B,TTLL12

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 FAR2

There's no related Drug.

Top

Cross referenced IDs for FAR2

* 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