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 FADS2
Basic gene info.Gene symbolFADS2
Gene namefatty acid desaturase 2
SynonymsD6D|DES6|FADSD6|LLCDL2|SLL0262|TU13
CytomapUCSC genome browser: 11q12.2
Genomic locationchr11 :61595712-61634825
Type of geneprotein-coding
RefGenesNM_001281501.1,
NM_001281502.1,NM_004265.3,
Ensembl idENSG00000134824
Descriptiondelta(6) desaturasedelta(6) fatty acid desaturasedelta-6 desaturasedelta-6 fatty acid desaturasedelta-6-desaturaselinoleoyl-CoA desaturase (delta-6-desaturase)-like 2
Modification date20141211
dbXrefs MIM : 606149
HGNC : HGNC
Ensembl : ENSG00000134824
HPRD : 05854
Vega : OTTHUMG00000163794
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FADS2
BioGPS: 9415
Gene Expression Atlas: ENSG00000134824
The Human Protein Atlas: ENSG00000134824
PathwayNCI Pathway Interaction Database: FADS2
KEGG: FADS2
REACTOME: FADS2
ConsensusPathDB
Pathway Commons: FADS2
MetabolismMetaCyc: FADS2
HUMANCyc: FADS2
RegulationEnsembl's Regulation: ENSG00000134824
miRBase: chr11 :61,595,712-61,634,825
TargetScan: NM_001281501
cisRED: ENSG00000134824
ContextiHOP: FADS2
cancer metabolism search in PubMed: FADS2
UCL Cancer Institute: FADS2
Assigned class in ccmGDBC

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Phenotypic Information for FADS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: FADS2
Familial Cancer Database: FADS2
* 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
KEGG_ALPHA_LINOLENIC_ACID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: FADS2
MedGen: FADS2 (Human Medical Genetics with Condition)
ClinVar: FADS2
PhenotypeMGI: FADS2 (International Mouse Phenotyping Consortium)
PhenomicDB: FADS2

Mutations for FADS2
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows FADS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ189008EZR1886159190821159190908FADS286270116163463661634820
BQ184412FADS218204116163463661634820EZR2022896159190821159190908
BU623713BOLA218283163000431630004581FADS2279688116163075461633216
CX787277SSRP11172115709355357093724FADS2165606116160533461615745
CN283539SAMD11401131867265867338FADS297572116163435361634823
BG742639GUK114981228333052228333551FADS2492907116163428561634704

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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=17)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=1)

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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
chr11:61615676-61615676p.A222T2
chr11:61632644-61632644p.R393Q2
chr11:61605297-61605297p.F85L2
chr11:61607997-61607997p.T170T2
chr11:61615706-61615706p.D232N2
chr11:61608140-61608140p.V187V2
chr11:61624491-61624491p.K251N2
chr11:61630533-61630533p.N324K2
chr11:61596030-61596030p.G56G2
chr11:61608179-61608179p.F200F2

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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
# sample17 121 1 2  411 166 5
# mutation17 111 1 2  411 166 5
nonsynonymous SNV14 10  1 2  311 134 2
synonymous SNV 3 11      1    32 3
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
chr11:61615706p.N302K,FADS22
chr11:61630533p.A200T,FADS22
chr11:61615676p.D210N,FADS22
chr11:61624947p.P254R,FADS21
chr11:61631214p.K387N,FADS21
chr11:61607877p.V165V,FADS21
chr11:61615699p.V267I,FADS21
chr11:61624985p.H173L,FADS21
chr11:61631244p.K269N,FADS21
chr11:61607902p.H35Y1

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 FADS2 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 FADS2

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

ACLY,LINC00263,CAMP,CCNE2,CDC45,CDC6,EXO1,
FADS1,FADS2,FAM111B,FDPS,FEN1,GANAB,MTUS1,
PGD,SCD,SREBF2,STIP1,TAAR1,TAAR8,UCHL5
ABCC12,ACSL3,ADAM2,AKR1D1,ALOX15B,APOD,C15orf43,
DHRS2,EPS8L3,FADS2,GGT1,HIST1H2AG,HPGD,IDI1,
IYD,LST-3TM12,RNASE12,SERHL,SRD5A1,TMPRSS11F,ZP2

ADAMTS19,ANTXR1,CRIP2,DKK3,DYTN,EDIL3,FADS1,
FADS2,FAM19A5,GPR68,LBH,LOXL1,NTM,PCSK9,
PDLIM4,SLCO4C1,SPOCK1,ST6GALNAC5,SULF1,TMEM217,VGLL3
ABCC9,ANXA6,BOC,MIR99AHG,CPEB1,EMP3,FADS2,
FRMD6,ITPR1,LGI2,MSN,PCDHGA2,PHGDH,PRAF2,
SCARA3,SEZ6L,SLC16A2,SULF1,SV2A,TACR1,VWA1
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 FADS2
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 2approved; nutraceuticalAlpha-Linolenic Acid


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Cross referenced IDs for FADS2
* 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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