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 ACSM3
Basic gene info.Gene symbolACSM3
Gene nameacyl-CoA synthetase medium-chain family member 3
SynonymsSA|SAH
CytomapUCSC genome browser: 16p13.11
Genomic locationchr16 :20775311-20797638
Type of geneprotein-coding
RefGenesNM_005622.3,
NM_202000.2,
Ensembl idENSG00000005187
DescriptionSA (rat hypertension-associated) homologSA hypertension-associated homologacyl-coenzyme A synthetase ACSM3, mitochondrialbutyrate--CoA ligase 3butyryl-coenzyme A synthetase 3middle-chain acyl-CoA synthetase 3protein SA homolog
Modification date20141207
dbXrefs MIM : 145505
HGNC : HGNC
Ensembl : ENSG00000005187
HPRD : 07033
Vega : OTTHUMG00000131552
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACSM3
BioGPS: 6296
Gene Expression Atlas: ENSG00000005187
The Human Protein Atlas: ENSG00000005187
PathwayNCI Pathway Interaction Database: ACSM3
KEGG: ACSM3
REACTOME: ACSM3
ConsensusPathDB
Pathway Commons: ACSM3
MetabolismMetaCyc: ACSM3
HUMANCyc: ACSM3
RegulationEnsembl's Regulation: ENSG00000005187
miRBase: chr16 :20,775,311-20,797,638
TargetScan: NM_005622
cisRED: ENSG00000005187
ContextiHOP: ACSM3
cancer metabolism search in PubMed: ACSM3
UCL Cancer Institute: ACSM3
Assigned class in ccmGDBC

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Phenotypic Information for ACSM3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACSM3
Familial Cancer Database: ACSM3
* 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: ACSM3
MedGen: ACSM3 (Human Medical Genetics with Condition)
ClinVar: ACSM3
PhenotypeMGI: ACSM3 (International Mouse Phenotyping Consortium)
PhenomicDB: ACSM3

Mutations for ACSM3
* 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 ACSM3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ316181MLH327416147548370375485719ACSM3411641162079210320792449

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=13

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=66)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr16:20803451-20803451p.G485V13
chr16:20793081-20793081p.R331*3
chr16:20796428-20796428p.T381M3
chr16:20803563-20803563p.R487Q3
chr16:20781479-20781479p.S41S3
chr16:20781555-20781555p.Q67*2
chr16:20781559-20781559p.W68*2
chr16:20796405-20796405p.Y373Y2
chr16:20792168-20792168p.S257S2
chr16:20803392-20803392p.M465I2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 81 4 21 442  74 13
# mutation11 71 4 21 542  74 17
nonsynonymous SNV 1 51 1 2  441  73 15
synonymous SNV1  2  3  1 1 1   1 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
chr16:20781479p.S41S,ACSM33
chr16:20796428p.R487Q2
chr16:20803563p.T381M,ACSM32
chr16:20796331p.K76N,ACSM31
chr16:20803324p.Q335R,ACSM31
chr16:20781506p.W472L1
chr16:20788733p.P78T,ACSM31
chr16:20807792p.K342T,ACSM31
chr16:20796340p.A475V1
chr16:20803376p.R88I,ACSM31

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 ACSM3 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 ACSM3

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

ACSM3,ADH1C,AFF2,AKR1B15,CHRNA2,EML5,EYS,
GNAL,ISX,IYD,KLRF1,KPNA7,LOC255167,ME1,
PLD5,RLN3,SC5D,SPINK8,SRD5A1,VSX2,WDR64
ABCC11,ABCC2,ACSM3,AFMID,AKR1D1,B3GAT1,C6orf223,
CHRNA2,CHST1,CLDN14,GSTT2,HMGCR,INSM2,LOC255167,
OR4N4,RIMS1,SLC5A11,SLCO1B1,SYCP1,TRPC7,ZP2

ACSM1,ACSM3,CRYM,GNG13,HTR3C,HTR3E,LOC100189589,
NPY6R,NXF3,OR2T34,PRH1,PRH2,RGS13,RGS21,
SH2D6,SH2D7,TAS1R1,TAS1R2,TCL6,THUMPD1,USP26
ACSM3,BSPRY,HMGN2P46,CDC25C,CEP70,CNOT10,COX5A,
EHF,ERLIN1,FRAT2,MLEC,MTIF2,MYB,RTN4IP1,
SCO1,STARD7,STIL,TAF5,TRIM34,WIPI1,ZNF695
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 ACSM3


There's no related Drug.
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Cross referenced IDs for ACSM3
* 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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