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 FADS2

Basic gene info.	Gene symbol	FADS2
	Gene name	fatty acid desaturase 2
	Synonyms	D6D\|DES6\|FADSD6\|LLCDL2\|SLL0262\|TU13
	Cytomap	UCSC genome browser: 11q12.2
	Genomic location	chr11 :61595712-61634825
	Type of gene	protein-coding
	RefGenes	NM_001281501.1, NM_001281502.1,NM_004265.3,
	Ensembl id	ENSG00000134824
	Description	delta(6) desaturasedelta(6) fatty acid desaturasedelta-6 desaturasedelta-6 fatty acid desaturasedelta-6-desaturaselinoleoyl-CoA desaturase (delta-6-desaturase)-like 2
	Modification date	20141211
dbXrefs	MIM : 606149
	HGNC : HGNC
	Ensembl : ENSG00000134824
	HPRD : 05854
	Vega : OTTHUMG00000163794
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FADS2
	BioGPS: 9415
	Gene Expression Atlas: ENSG00000134824
	The Human Protein Atlas: ENSG00000134824
Pathway	NCI Pathway Interaction Database: FADS2
	KEGG: FADS2
	REACTOME: FADS2
	ConsensusPathDB
	Pathway Commons: FADS2
Metabolism	MetaCyc: FADS2
	HUMANCyc: FADS2
Regulation	Ensembl's Regulation: ENSG00000134824
	miRBase: chr11 :61,595,712-61,634,825
	TargetScan: NM_001281501
	cisRED: ENSG00000134824
Context	iHOP: FADS2
	cancer metabolism search in PubMed: FADS2
	UCL Cancer Institute: FADS2
Assigned class in ccmGDB	C

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Phenotypic Information for FADS2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_ALPHA_LINOLENIC_ACID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: FADS2
	MedGen: FADS2 (Human Medical Genetics with Condition)
	ClinVar: FADS2
Phenotype	MGI: FADS2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows FADS2 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
BQ189008	EZR	1	88	6	159190821	159190908	FADS2	86	270	11	61634636	61634820
BQ184412	FADS2	18	204	11	61634636	61634820	EZR	202	289	6	159190821	159190908
BU623713	BOLA2	18	283	16	30004316	30004581	FADS2	279	688	11	61630754	61633216
CX787277	SSRP1	1	172	11	57093553	57093724	FADS2	165	606	11	61605334	61615745
CN283539	SAMD11	40	113	1	867265	867338	FADS2	97	572	11	61634353	61634823
BG742639	GUK1	1	498	1	228333052	228333551	FADS2	492	907	11	61634285	61634704

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

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

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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=3

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Somatic 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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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
chr11:61596030-61596030	p.G56G	2
chr11:61608179-61608179	p.F200F	2
chr11:61615659-61615659	p.R216H	2
chr11:61596061-61596061	p.D67Y	2
chr11:61630798-61630798	p.H342P	2
chr11:61615676-61615676	p.A222T	2
chr11:61632644-61632644	p.R393Q	2
chr11:61605297-61605297	p.F85L	2
chr11:61607997-61607997	p.T170T	2
chr11:61615706-61615706	p.D232N	2

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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	1	7		12	1		1		2			4	1	1		1	6	6		5
# mutation	1	7		11	1		1		2			4	1	1		1	6	6		5
nonsynonymous SNV	1	4		10			1		2			3	1	1		1	3	4		2
synonymous SNV		3		1	1							1					3	2		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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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
chr11:61615676	p.N302K,FADS2	2
chr11:61615706	p.A200T,FADS2	2
chr11:61630533	p.D210N,FADS2	2
chr11:61605261	p.H117Y,FADS2	1
chr11:61630802	p.K229N,FADS2	1
chr11:61608167	p.F359F,FADS2	1
chr11:61624518	p.H117L,FADS2	1
chr11:61605272	p.N238N,FADS2	1
chr11:61630830	p.R371Q,FADS2	1
chr11:61608169	p.W155C,FADS2	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 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

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


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

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 FADS2

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 2	approved; nutraceutical	Alpha-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