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 ACSL1
Basic gene info.Gene symbolACSL1
Gene nameacyl-CoA synthetase long-chain family member 1
SynonymsACS1|FACL1|FACL2|LACS|LACS1|LACS2
CytomapUCSC genome browser: 4q35.1
Genomic locationchr4 :185676748-185747215
Type of geneprotein-coding
RefGenesNM_001286708.1,
NM_001286710.1,NM_001286711.1,NM_001286712.1,NM_001995.3,
Ensembl idENSG00000151726
DescriptionLACS 1LACS 2acyl-CoA synthetase 1fatty-acid-Coenzyme A ligase, long-chain 1fatty-acid-Coenzyme A ligase, long-chain 2lignoceroyl-CoA synthaselong-chain acyl-CoA synthetase 1long-chain acyl-CoA synthetase 2long-chain fatty acid-CoA ligase 2long-ch
Modification date20141207
dbXrefs MIM : 152425
HGNC : HGNC
Ensembl : ENSG00000151726
HPRD : 01068
Vega : OTTHUMG00000160547
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACSL1
BioGPS: 2180
Gene Expression Atlas: ENSG00000151726
The Human Protein Atlas: ENSG00000151726
PathwayNCI Pathway Interaction Database: ACSL1
KEGG: ACSL1
REACTOME: ACSL1
ConsensusPathDB
Pathway Commons: ACSL1
MetabolismMetaCyc: ACSL1
HUMANCyc: ACSL1
RegulationEnsembl's Regulation: ENSG00000151726
miRBase: chr4 :185,676,748-185,747,215
TargetScan: NM_001286708
cisRED: ENSG00000151726
ContextiHOP: ACSL1
cancer metabolism search in PubMed: ACSL1
UCL Cancer Institute: ACSL1
Assigned class in ccmGDBC

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Phenotypic Information for ACSL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACSL1
Familial Cancer Database: ACSL1
* 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
Orphanet
DiseaseKEGG Disease: ACSL1
MedGen: ACSL1 (Human Medical Genetics with Condition)
ClinVar: ACSL1
PhenotypeMGI: ACSL1 (International Mouse Phenotyping Consortium)
PhenomicDB: ACSL1

Mutations for ACSL1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ACSL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI020982MPO12178175635566756355832ACSL11714804185677924185678233

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=72)
Stat. for Synonymous SNVs
(# total SNVs=20)
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
chr4:185724638-185724638p.R11*4
chr4:185684329-185684329p.E505K2
chr4:185681557-185681557p.R579Q2
chr4:185695007-185695007p.R260Q2
chr4:185684398-185684398p.A482S2
chr4:185697670-185697670p.G242W2
chr4:185687863-185687863p.F392F2
chr4:185678418-185678418p.V653G2
chr4:185697722-185697722p.I224M1
chr4:185678828-185678828p.V639V1

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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
# sample 1191 1 41 1431  82 9
# mutation 11111 1 41 1531  82 14
nonsynonymous SNV  171 1 31 1121  32 12
synonymous SNV 1 4    1  41   5  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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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
chr4:185697670p.G106G,ACSL12
chr4:185705138p.G208W,ACSL12
chr4:185679022p.P333L,ACSL11
chr4:185697653p.L174L,ACSL11
chr4:185709801p.M12V,ACSL11
chr4:185686012p.K527N,ACSL11
chr4:185724659p.P326P,ACSL11
chr4:185678285p.I140I,ACSL11
chr4:185689518p.H4Y,ACSL11
chr4:185679038p.K663N,ACSL11

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 ACSL1 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 ACSL1

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

AADAT,ACSL1,AKR1B15,AKR1D1,ATP13A4,C6orf223,CLDN8,
FCN2,FKBP5,GRAMD2,IDI1,LST-3TM12,MYOM2,NAMPT,
PNLIPRP3,RLN3,RNASE12,SC5D,SLC41A2,SPINK8,SRD5A1
ABCD2,ACACB,ACOT1,ACOT2,ACSL1,ACSS2,BOK,
CIDEC,DGAT1,FAH,GBE1,GPAM,GYG2,HEPACAM,
HEPN1,LGALS12,LPL,MARC1,MTHFD1,PDE3B,PECR

ACSL1,ALPL,C5AR1,CD163,CD209,EBF2,F13A1,
FCGR2A,FCN1,FPR1,GFPT2,GNS,HEG1,HRH2,
LILRA6,LOX,NLRC4,NRP1,PCDHGA12,RASGRP4,SLC1A3
ACSL1,C6orf223,CACNA1E,DGAT2,DZIP1L,FASN,FCN2,
GPAM,GYS2,HTR5A,LGALS12,LPL,MRAP,PLIN5,
PLXNA4,SAA1,SAA2,SCD,SH3RF3,SPINK13,THRSP
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 ACSL1
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
DB00131acyl-CoA synthetase long-chain family member 1approved; nutraceuticalAdenosine monophosphate
DB00171acyl-CoA synthetase long-chain family member 1approved; nutraceuticalAdenosine triphosphate
DB00367acyl-CoA synthetase long-chain family member 1approved; investigationalLevonorgestrel


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Cross referenced IDs for ACSL1
* 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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