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 ACSL3

Basic gene info.	Gene symbol	ACSL3
	Gene name	acyl-CoA synthetase long-chain family member 3
	Synonyms	ACS3\|FACL3\|PRO2194
	Cytomap	UCSC genome browser: 2q34-q35
	Genomic location	chr2 :223725731-223808119
	Type of gene	protein-coding
	RefGenes	NM_004457.3, NM_203372.1,
	Ensembl id	ENSG00000123983
	Description	LACS 3fatty-acid-Coenzyme A ligase, long-chain 3lignoceroyl-CoA synthaselong-chain acyl-CoA synthetase 3long-chain-fatty-acid--CoA ligase 3
	Modification date	20141207
dbXrefs	MIM : 602371
	HGNC : HGNC
	HPRD : 03845
Protein	UniProt: O95573 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ACSL3
	BioGPS: 2181
	Gene Expression Atlas: ENSG00000123983
	The Human Protein Atlas: ENSG00000123983
Pathway	NCI Pathway Interaction Database: ACSL3
	KEGG: ACSL3
	REACTOME: ACSL3
	ConsensusPathDB
	Pathway Commons: ACSL3
Metabolism	MetaCyc: ACSL3
	HUMANCyc: ACSL3
Regulation	Ensembl's Regulation: ENSG00000123983
	miRBase: chr2 :223,725,731-223,808,119
	TargetScan: NM_004457
	cisRED: ENSG00000123983
Context	iHOP: ACSL3
	cancer metabolism search in PubMed: ACSL3
	UCL Cancer Institute: ACSL3
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ACSL3 in cancer cell metabolism	1. Cadenas C, Vosbeck S, Hein EM, Hellwig B, Langer A, et al. (2012) Glycerophospholipid profile in oncogene-induced senescence. Biochim Biophys Acta 1821: 1256-1268. doi: 10.1016/j.bbalip.2011.11.008. go to article 2. 1. Sumantran VN, Mishra P, Sudhakar N (2015) Microarray analysis of differentially expressed genes regulating lipid metabolism during melanoma progression. Indian J Biochem Biophys 52: 125-131. go to article

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Phenotypic Information for ACSL3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ACSL3
	Familial Cancer Database: ACSL3

* 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_FATTY_ACID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	602371; gene.
Orphanet
Disease	KEGG Disease: ACSL3
	MedGen: ACSL3 (Human Medical Genetics with Condition)
	ClinVar: ACSL3
Phenotype	MGI: ACSL3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ACSL3

Mutations for ACSL3

* 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

* 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ACSL3	chr2	223731485	223731505	TMEM132A	chr11	60704441	60704461
ovary	ACSL3	chr2	223766141	223766161	ACSL3	chr2	223767093	223767113

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 ACSL3 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
BQ343112	ACSL3	222	266	2	223773788	223773832	MKI67IP	265	634	2	122488497	122493267
BM684664	ACSL3	1	82	2	223807733	223807814	ACSL3	78	613	2	223807994	223808529

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=49)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr2:223782769-223782769	p.T188S	6
chr2:223806250-223806250	p.R681C	5
chr2:223799373-223799373	p.V658A	4
chr2:223783810-223783810	p.R232Q	3
chr2:223786008-223786008	p.P272P	3
chr2:223781078-223781078	p.V140V	2
chr2:223782762-223782762	p.?	2
chr2:223786007-223786007	p.P272L	2
chr2:223773807-223773807	p.G106E	2
chr2:223773856-223773856	p.K122N	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=4

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		16	1		1		1			3	2	2			4	6		8
# mutation		1		12	1		1		1			3	2	2			4	6		9
nonsynonymous SNV		1		9	1		1		1			3	2	2			3	5		8
synonymous SNV				3													1	1		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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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
chr2:223799373	p.V658A,ACSL3	4
chr2:223806250	p.R681C,ACSL3	3
chr2:223773807	p.G106E,ACSL3	3
chr2:223786008	p.P272P,ACSL3	3
chr2:223786007	p.P272L,ACSL3	2
chr2:223783804	p.P40S,ACSL3	1
chr2:223791784	p.L277S,ACSL3	1
chr2:223773608	p.R54Q,ACSL3	1
chr2:223783810	p.G307G,ACSL3	1
chr2:223791818	p.S670N,ACSL3	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 ACSL3 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 ACSL3

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


AACS,ACSL3,ACSM1,AKR1D1,B3GAT1,C15orf43,FCN2, GSTM5,IDI1,ISX,LST-3TM12,PNLIPRP3,RNASE11,RNASE12, SC5D,SCP2,SLCO1B1,SULT1C3,TMIGD1,TMPRSS9,ZNF652	ABCC11,ACSL3,ADAM2,ALOX15B,B3GAT1,C15orf43,DHRS2, GGT1,HPGD,IDI1,MPV17L,NSUN2,PNLIPRP3,RNASE12, SERHL2,SERHL,SLC15A1,SRD5A1,TMPRSS11F,UGT2B10,UGT2B11

ACSL3,CNOT11,CKAP2L,CYP51A1,DHCR7,ELOVL6,HMGCR, HMGCS1,IDI1,PPIG,DESI2,PRPF40A,RAB10,RAB1A, MSMO1,SC5D,SCD,SH3BP4,STARD4,TMEM135,XRCC5	ACBD3,ACSL3,AP2B1,ASCC3,ATR,CKAP4,CYP51A1, DHCR7,DNAJC10,EMP2,FGFBP1,GSPT1,HNRNPR,HSP90B1, KPNB1,LARP4,PDE11A,RDH11,SQLE,STT3A,UGGT1

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 ACSL3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA27967; -.
Organism-specific databases	CTD	2181; -.

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
DB00159	acyl-CoA synthetase long-chain family member 3	approved; nutraceutical	Icosapent

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Cross referenced IDs for ACSL3

* 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