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 FADS1

Basic gene info.	Gene symbol	FADS1
	Gene name	fatty acid desaturase 1
	Synonyms	D5D\|FADS6\|FADSD5\|LLCDL1\|TU12
	Cytomap	UCSC genome browser: 11q12.2-q13.1
	Genomic location	chr11 :61567096-61584529
	Type of gene	protein-coding
	RefGenes	NM_013402.4,
	Ensembl id	ENSG00000149485
	Description	delta(5) desaturasedelta(5) fatty acid desaturasedelta-5 desaturasedelta-5 fatty acid desaturaselinoleoyl-CoA desaturase (delta-6-desaturase)-like 1
	Modification date	20141222
dbXrefs	MIM : 606148
	HGNC : HGNC
	Ensembl : ENSG00000149485
	HPRD : 06935
	Vega : OTTHUMG00000157155
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FADS1
	BioGPS: 3992
	Gene Expression Atlas: ENSG00000149485
	The Human Protein Atlas: ENSG00000149485
Pathway	NCI Pathway Interaction Database: FADS1
	KEGG: FADS1
	REACTOME: FADS1
	ConsensusPathDB
	Pathway Commons: FADS1
Metabolism	MetaCyc: FADS1
	HUMANCyc: FADS1
Regulation	Ensembl's Regulation: ENSG00000149485
	miRBase: chr11 :61,567,096-61,584,529
	TargetScan: NM_013402
	cisRED: ENSG00000149485
Context	iHOP: FADS1
	cancer metabolism search in PubMed: FADS1
	UCL Cancer Institute: FADS1
Assigned class in ccmGDB	C

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Phenotypic Information for FADS1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: FADS1
	MedGen: FADS1 (Human Medical Genetics with Condition)
	ClinVar: FADS1
Phenotype	MGI: FADS1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows FADS1 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
AW579368	FADS1	15	97	11	61570504	61570587	FADS1	95	240	11	61569706	61569851
BG289620	FADS1	1	311	11	61568978	61569290	CLDN1	303	769	3	190024204	190024669
AI937735	LOC440944	2	214	3	9426340	9426552	FADS1	212	392	11	61580785	61584167
BE789742	FADS1	1	52	11	61568454	61568505	FADS1	49	718	11	61567747	61568421
AW937108	FADS1	62	163	11	61569592	61569695	YWHAE	154	512	17	1270940	1271298
CB143399	FADS1	14	288	11	61569355	61569629	TGOLN2	286	512	2	85545198	85545424
N67724	FADS1	1	61	11	61569748	61569808	VGLL3	53	457	3	86994531	86994935

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=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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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
chr11:61569884-61569884	p.445	2
chr11:61578255-61578255	p.F238V	1
chr11:61580763-61580763	p.L89L	1
chr11:61569896-61569896	p.Y441C	1
chr11:61578274-61578274	p.D231E	1
chr11:61580784-61580784	p.K82K	1
chr11:61570286-61570286	p.A424T	1
chr11:61578278-61578287	p.R227fs*39	1
chr11:61580785-61580785	p.K82T	1
chr11:61570315-61570315	p.Y414C	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=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			1						1		1	1			1		1		4
# mutation	2			1						1		1	1			1		1		6
nonsynonymous SNV	1									1			1					1		4
synonymous SNV	1			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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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
chr11:61580784	p.N422N	1
chr11:61570566	p.P315P	1
chr11:61584180	p.M314V	1
chr11:61574167	p.F295L	1
chr11:61574172	p.F295V	1
chr11:61578253	p.D288E	1
chr11:61578255	p.P265P	1
chr11:61578274	p.L198L	1
chr11:61578343	p.M182I	1
chr11:61580035	p.E153D	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 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

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


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

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 FADS1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00132	fatty acid desaturase 1	approved; nutraceutical	Alpha-Linolenic Acid
DB00159	fatty acid desaturase 1	approved; nutraceutical	Icosapent

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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