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 ACSM1
Basic gene info.Gene symbolACSM1
Gene nameacyl-CoA synthetase medium-chain family member 1
SynonymsBUCS1|MACS1
CytomapUCSC genome browser: 16p12.3
Genomic locationchr16 :20634558-20702578
Type of geneprotein-coding
RefGenesNM_052956.2,
Ensembl idENSG00000166743
DescriptionButyrate CoA ligaseacyl-coenzyme A synthetase ACSM1, mitochondrialbutyrate--CoA ligase 1butyryl Coenzyme A synthetase 1butyryl-coenzyme A synthetase 1lipoate-activating enzymemedium-chain acyl-CoA synthetasemiddle-chain acyl-CoA synthetase 1
Modification date20141207
dbXrefs MIM : 614357
HGNC : HGNC
Ensembl : ENSG00000166743
HPRD : 12551
Vega : OTTHUMG00000131550
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACSM1
BioGPS: 116285
Gene Expression Atlas: ENSG00000166743
The Human Protein Atlas: ENSG00000166743
PathwayNCI Pathway Interaction Database: ACSM1
KEGG: ACSM1
REACTOME: ACSM1
ConsensusPathDB
Pathway Commons: ACSM1
MetabolismMetaCyc: ACSM1
HUMANCyc: ACSM1
RegulationEnsembl's Regulation: ENSG00000166743
miRBase: chr16 :20,634,558-20,702,578
TargetScan: NM_052956
cisRED: ENSG00000166743
ContextiHOP: ACSM1
cancer metabolism search in PubMed: ACSM1
UCL Cancer Institute: ACSM1
Assigned class in ccmGDBC

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Phenotypic Information for ACSM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACSM1
Familial Cancer Database: ACSM1
* 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_BUTANOATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACSM1
MedGen: ACSM1 (Human Medical Genetics with Condition)
ClinVar: ACSM1
PhenotypeMGI: ACSM1 (International Mouse Phenotyping Consortium)
PhenomicDB: ACSM1

Mutations for ACSM1
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryACSM1chr162065576420655784ACSM1chr162065758020657600
ovaryACSM1chr162070208220702102ACSM1chr162068241720682437
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 ACSM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF932027KAT2A13184174026539040265561ACSM1172192162068819420688214

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)1                
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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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=62)
Stat. for Synonymous SNVs
(# total SNVs=36)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr16:20673143-20673143p.R322L6
chr16:20696520-20696520p.R133Q4
chr16:20702394-20702394p.R39R3
chr16:20638573-20638573p.K455N3
chr16:20648698-20648698p.V398I3
chr16:20702428-20702428p.R28H2
chr16:20648726-20648726p.F388F2
chr16:20638635-20638635p.D435N2
chr16:20702464-20702464p.S16F2
chr16:20636840-20636840p.R478C2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 132 3 2  13111  404 14
# mutation 1 112 3 2  12111  435 15
nonsynonymous SNV   81 2    66   233 8
synonymous SNV 1 31 1 2  651  202 7
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
chr16:20702394p.R133Q3
chr16:20696520p.R39R3
chr16:20638573p.K455K3
chr16:20673143p.F329F2
chr16:20648732p.P505P2
chr16:20681188p.R322Q2
chr16:20638543p.E573K2
chr16:20673121p.I291I2
chr16:20634825p.R28H2
chr16:20702428p.L465L2

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 ACSM1 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 ACSM1

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

ACSM1,B3GAT1,C15orf43,CLDN8,FCN2,GGT1,GGT3P,
GUSB,ISX,LST-3TM12,MYOM2,PNLIPRP3,RLN3,SCP2,
SERHL2,SERHL,SLC38A4,SLCO1B1,SPINK8,SULT1C3,UGT2B28
ABCC12,ACSM1,ADCY10,LINC00589,CHRNA2,CTNNA2,DDC,
ELOVL7,EPS8L3,GSTTP1,HIST1H2AL,HIST1H2BJ,HIST1H3G,IYD,
LOC285692,LOC643486,OR10A7,OR10S1,OR52E8,RIMS1,SLC12A3

ACSM1,ACSM3,ALDH1L1,APOBR,SMCO4,HMGN2P46,C2orf72,
CES3,CYB561,ERN2,GJA9,MOGAT2,MRAP2,NXF3,
SGSM3,SH3RF2,SLC9A2,TXNDC11,VSIG2,VWA5A,ZBTB7C
ACSM1,LINC00323,CXCR2P1,CYP4F22,DGCR11,EN1,FAM138D,
FLJ45983,G3BP2,HERC5,KIR3DL1,KLK8,KRTAP5-8,LAG3,
LEPROTL1,MYEOV,NLRP10,PADI6,SH2D4B,SLC9C2,TSGA13
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 ACSM1
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 medium-chain family member 1approved; nutraceuticalAdenosine monophosphate
DB00171acyl-CoA synthetase medium-chain family member 1approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for ACSM1
* 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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