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 symbolFAR1
Gene namefatty acyl CoA reductase 1
SynonymsMLSTD2|SDR10E1
CytomapUCSC genome browser: 11p15.2
Genomic locationchr11 :13690205-13753893
Type of geneprotein-coding
RefGenesNM_032228.5,
Ensembl idENSG00000197601
Descriptionfatty acyl-CoA reductase 1male sterility domain containing 2male sterility domain-containing protein 2putative fatty acyl reductaseshort chain dehydrogenase/reductase family 10E, member 1
Modification date20141207
dbXrefs MIM : 616107
HGNC : HGNC
Ensembl : ENSG00000197601
HPRD : 14724
Vega : OTTHUMG00000165743
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FAR1
BioGPS: 84188
Gene Expression Atlas: ENSG00000197601
The Human Protein Atlas: ENSG00000197601
PathwayNCI Pathway Interaction Database: FAR1
KEGG: FAR1
REACTOME: FAR1
ConsensusPathDB
Pathway Commons: FAR1
MetabolismMetaCyc: FAR1
HUMANCyc: FAR1
RegulationEnsembl's Regulation: ENSG00000197601
miRBase: chr11 :13,690,205-13,753,893
TargetScan: NM_032228
cisRED: ENSG00000197601
ContextiHOP: FAR1
cancer metabolism search in PubMed: FAR1
UCL Cancer Institute: FAR1
Assigned class in ccmGDBC

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Phenotypic Information for FAR1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_PEROXISOMAL_LIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: FAR1
MedGen: FAR1 (Human Medical Genetics with Condition)
ClinVar: FAR1
PhenotypeMGI: FAR1 (International Mouse Phenotyping Consortium)
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.

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
ovaryFAR1chr111369709213697112FAR1chr111369730313697323
ovaryFAR1chr111374636113746381FAR1chr111375159813751618
pancreasFAR1chr111369992713699947SPON1chr111411941514119435
pancreasFAR1chr111369992713699947SPON1chr111411941714119437
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 FAR1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE707585PHKB1136164773325147733387FAR1128292111374915713750249
AA862191FAR1975111369456013694626FAR164212111369442313694571
DA215427CTNNB1317334124099241241162FAR1171538111374327513750266
BF906017FAR1197111369548213695580FAR192408111369208913692402
BI019366FAR1199111369548213695580FAR194360111369208913692352
BI019383FAR1199111369548213695580FAR194442111369208913692434

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        2        
GAIN (# sample)        2        
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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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=2

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check002.gifSomatic 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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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
chr11:13733493-13733493p.R263*3
chr11:13729529-13729529p.H150Y2
chr11:13721922-13721922p.N83S2
chr11:13729478-13729478p.R133*2
chr11:13733566-13733566p.A287V1
chr11:13721879-13721880p.R69fs*141
chr11:13729486-13729486p.L135L1
chr11:13736181-13736181p.A361T1
chr11:13732391-13732391p.G233S1
chr11:13749204-13749204p.L453L1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 3  3 2  421  36 6
# mutation31 3  3 2  421  46 6
nonsynonymous SNV2  2  3 1  311  23 5
synonymous SNV11 1    1  11   23 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
chr11:13743367p.A387S1
chr11:13729486p.S180S1
chr11:13734528p.S398Y1
chr11:13749116p.L196L1
chr11:13729544p.T403I1
chr11:13734540p.R200K1
chr11:13749118p.V406V1
chr11:13729621p.S230S1
chr11:13734550p.D424V1
chr11:13749138p.G233S1

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 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

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

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
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 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



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