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 FADS1
Basic gene info.Gene symbolFADS1
Gene namefatty acid desaturase 1
SynonymsD5D|FADS6|FADSD5|LLCDL1|TU12
CytomapUCSC genome browser: 11q12.2-q13.1
Genomic locationchr11 :61567096-61584529
Type of geneprotein-coding
RefGenesNM_013402.4,
Ensembl idENSG00000149485
Descriptiondelta(5) desaturasedelta(5) fatty acid desaturasedelta-5 desaturasedelta-5 fatty acid desaturaselinoleoyl-CoA desaturase (delta-6-desaturase)-like 1
Modification date20141222
dbXrefs MIM : 606148
HGNC : HGNC
Ensembl : ENSG00000149485
HPRD : 06935
Vega : OTTHUMG00000157155
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FADS1
BioGPS: 3992
Gene Expression Atlas: ENSG00000149485
The Human Protein Atlas: ENSG00000149485
PathwayNCI Pathway Interaction Database: FADS1
KEGG: FADS1
REACTOME: FADS1
ConsensusPathDB
Pathway Commons: FADS1
MetabolismMetaCyc: FADS1
HUMANCyc: FADS1
RegulationEnsembl's Regulation: ENSG00000149485
miRBase: chr11 :61,567,096-61,584,529
TargetScan: NM_013402
cisRED: ENSG00000149485
ContextiHOP: FADS1
cancer metabolism search in PubMed: FADS1
UCL Cancer Institute: FADS1
Assigned class in ccmGDBC

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Phenotypic Information for FADS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: FADS1
Familial Cancer Database: FADS1
* 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_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: FADS1
MedGen: FADS1 (Human Medical Genetics with Condition)
ClinVar: FADS1
PhenotypeMGI: FADS1 (International Mouse Phenotyping Consortium)
PhenomicDB: FADS1

Mutations for FADS1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows FADS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW579368FADS11597116157050461570587FADS195240116156970661569851
BG289620FADS11311116156897861569290CLDN13037693190024204190024669
AI937735LOC4409442214394263409426552FADS1212392116158078561584167
BE789742FADS1152116156845461568505FADS149718116156774761568421
AW937108FADS162163116156959261569695YWHAE1545121712709401271298
CB143399FADS114288116156935561569629TGOLN228651228554519885545424
N67724FADS1161116156974861569808VGLL35345738699453186994935

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   1    1 1      
GAIN (# sample)   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)

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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=13)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted 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
chr11:61569884-61569884p.*445*2
chr11:61578253-61578253p.F238L1
chr11:61580747-61580747p.P95A1
chr11:61569894-61569894p.L442I1
chr11:61578255-61578255p.F238V1
chr11:61580763-61580763p.L89L1
chr11:61569896-61569896p.Y441C1
chr11:61578274-61578274p.D231E1
chr11:61580784-61580784p.K82K1
chr11:61570286-61570286p.A424T1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  1     1 11  1 1 4
# mutation2  1     1 11  1 1 6
nonsynonymous SNV1        1  1    1 4
synonymous SNV1  1       1   1   2
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
chr11:61569896p.Y498C1
chr11:61580742p.Y471C1
chr11:61570315p.N422N1
chr11:61580784p.P315P1
chr11:61570566p.M314V1
chr11:61584180p.F295L1
chr11:61574167p.F295V1
chr11:61574172p.D288E1
chr11:61578253p.P265P1
chr11:61578255p.L198L1

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 FADS1 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 FADS1

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

ARPP21,C5orf60,CARD16,CBX8,DNAJC1,FADS1,FADS2,
FEN1,FTH1,FTH1P3,KRTAP10-3,MYBPC3,OR5D16,PGA3,
SCD,SDHAF2,SPDYC,SULT1A1,SULT1A2,TNFRSF18,TTTY4C
ACACA,ACLY,ACSS2,C8orf34,CDKN2C,CPA2,CRHBP,
DMRTA1,ECHDC1,ELOVL6,FADS1,FASN,GPR50,ME1,
NKX2-4,OLFM2,SCD,SEL1L2,SPZ1,TF,TMEM132B

CPSF7,DCHS1,DENND5A,ELOVL5,FADS1,FADS2,FADS3,
FAM126A,GDF11,GPR68,GSTT2,LBH,NDRG4,NT5DC2,
PCSK9,RAB3IL1,RDH11,SLC2A6,TMEM109,VPS37C,VWCE
ARL9,LURAP1,MIR99AHG,CALU,ELOVL5,FADS1,FKBP14,
GDF11,GMPR,GNB4,GUCY1B3,KCND3,MRAS,NRSN2,
PRAF2,PTP4A3,RAB31,SULF1,TMEM45A,ZCCHC24,ZNF385D
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 FADS1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00132fatty acid desaturase 1approved; nutraceuticalAlpha-Linolenic Acid
DB00159fatty acid desaturase 1approved; nutraceuticalIcosapent


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Cross referenced IDs for FADS1
* 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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