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 symbolACSL3
Gene nameacyl-CoA synthetase long-chain family member 3
SynonymsACS3|FACL3|PRO2194
CytomapUCSC genome browser: 2q34-q35
Genomic locationchr2 :223725731-223808119
Type of geneprotein-coding
RefGenesNM_004457.3,
NM_203372.1,
Ensembl idENSG00000123983
DescriptionLACS 3fatty-acid-Coenzyme A ligase, long-chain 3lignoceroyl-CoA synthaselong-chain acyl-CoA synthetase 3long-chain-fatty-acid--CoA ligase 3
Modification date20141207
dbXrefs MIM : 602371
HGNC : HGNC
HPRD : 03845
ProteinUniProt: O95573
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACSL3
BioGPS: 2181
Gene Expression Atlas: ENSG00000123983
The Human Protein Atlas: ENSG00000123983
PathwayNCI Pathway Interaction Database: ACSL3
KEGG: ACSL3
REACTOME: ACSL3
ConsensusPathDB
Pathway Commons: ACSL3
MetabolismMetaCyc: ACSL3
HUMANCyc: ACSL3
RegulationEnsembl's Regulation: ENSG00000123983
miRBase: chr2 :223,725,731-223,808,119
TargetScan: NM_004457
cisRED: ENSG00000123983
ContextiHOP: ACSL3
cancer metabolism search in PubMed: ACSL3
UCL Cancer Institute: ACSL3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ACSL3 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_FATTY_ACID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602371; gene.
Orphanet
DiseaseKEGG Disease: ACSL3
MedGen: ACSL3 (Human Medical Genetics with Condition)
ClinVar: ACSL3
PhenotypeMGI: ACSL3 (International Mouse Phenotyping Consortium)
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.

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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryACSL3chr2223731485223731505TMEM132Achr116070444160704461
ovaryACSL3chr2223766141223766161ACSL3chr2223767093223767113
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 ACSL3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ343112ACSL32222662223773788223773832MKI67IP2656342122488497122493267
BM684664ACSL31822223807733223807814ACSL3786132223807994223808529

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=6

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check002.gifSomatic 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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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
chr2:223782769-223782769p.T188S6
chr2:223806250-223806250p.R681C5
chr2:223799373-223799373p.V658A4
chr2:223783810-223783810p.R232Q3
chr2:223786008-223786008p.P272P3
chr2:223781078-223781078p.V140V2
chr2:223782762-223782762p.?2
chr2:223786007-223786007p.P272L2
chr2:223773807-223773807p.G106E2
chr2:223783804-223783804p.R230H1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 161 1 1  322  46 8
# mutation 1 121 1 1  322  46 9
nonsynonymous SNV 1 91 1 1  322  35 8
synonymous SNV   3            11 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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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
chr2:223799373p.V658A,ACSL34
chr2:223806250p.R681C,ACSL33
chr2:223773807p.G106E,ACSL33
chr2:223786008p.P272P,ACSL33
chr2:223786007p.P272L,ACSL32
chr2:223787865p.P40S,ACSL31
chr2:223773571p.L277S,ACSL31
chr2:223799360p.R54Q,ACSL31
chr2:223783804p.G307G,ACSL31
chr2:223791784p.S670N,ACSL31

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 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

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

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
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 ACSL3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA27967; -.
Organism-specific databasesCTD 2181; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00159acyl-CoA synthetase long-chain family member 3approved; nutraceuticalIcosapent


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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



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