Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 ACAA1
Basic gene info.Gene symbolACAA1
Gene nameacetyl-CoA acyltransferase 1
SynonymsACAA|PTHIO|THIO
CytomapUCSC genome browser: 3p22.2
Genomic locationchr3 :38164200-38178733
Type of geneprotein-coding
RefGenesNM_001130410.1,
NM_001607.3,NR_024024.1,
Ensembl idENSG00000060971
Description3-ketoacyl-CoA thiolase, peroxisomalacetyl-Coenzyme A acyltransferase 1beta-ketothiolaseperoxisomal 3-oxoacyl-CoA thiolaseperoxisomal 3-oxoacyl-Coenzyme A thiolase
Modification date20141207
dbXrefs MIM : 604054
HGNC : HGNC
Ensembl : ENSG00000060971
HPRD : 06815
Vega : OTTHUMG00000131087
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACAA1
BioGPS: 30
Gene Expression Atlas: ENSG00000060971
The Human Protein Atlas: ENSG00000060971
PathwayNCI Pathway Interaction Database: ACAA1
KEGG: ACAA1
REACTOME: ACAA1
ConsensusPathDB
Pathway Commons: ACAA1
MetabolismMetaCyc: ACAA1
HUMANCyc: ACAA1
RegulationEnsembl's Regulation: ENSG00000060971
miRBase: chr3 :38,164,200-38,178,733
TargetScan: NM_001130410
cisRED: ENSG00000060971
ContextiHOP: ACAA1
cancer metabolism search in PubMed: ACAA1
UCL Cancer Institute: ACAA1
Assigned class in ccmGDBC

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Phenotypic Information for ACAA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACAA1
Familial Cancer Database: ACAA1
* 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_PEROXISOMAL_LIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACAA1
MedGen: ACAA1 (Human Medical Genetics with Condition)
ClinVar: ACAA1
PhenotypeMGI: ACAA1 (International Mouse Phenotyping Consortium)
PhenomicDB: ACAA1

Mutations for ACAA1
* 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 ACAA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA055429PYGB1514202522891825255316ACAA151458133816801138168078
AA405551ACAA15327833816731838167810ACAA127640733816803038168161
BF859008ACAA13025433816814638170880ACAA124933433816805738168142

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=20)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr3:38167184-38167184p.E357D2
chr3:38167344-38167344p.F342F2
chr3:38173449-38173449p.S124L2
chr3:38169314-38169314p.E197K2
chr3:38164614-38164614p.?2
chr3:38167784-38167784p.R289Q2
chr3:38167138-38167138p.V373M2
chr3:38168072-38168072p.R249H1
chr3:38173085-38173085p.?1
chr3:38167177-38167177p.R360*1

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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
# sample1  81    2 111 153 4
# mutation1  81    2 111 153 4
nonsynonymous SNV1  61    2  1  151 4
synonymous SNV   2       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
chr3:38175457p.I103I,ACAA12
chr3:38169329p.D199N,ACAA11
chr3:38167755p.G97E,ACAA11
chr3:38170828p.T196T,ACAA11
chr3:38167802p.V72L,ACAA11
chr3:38173094p.I190V,ACAA11
chr3:38168013p.F186L,ACAA11
chr3:38173446p.G184V,ACAA11
chr3:38164583p.G317G,ACAA11
chr3:38168124p.E164K,ACAA11

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 ACAA1 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 ACAA1

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

ABHD14A,ACAA1,ACY1,AZGP1,ELP6,CCDC12,CYB561D2,
DCXR,DHRS4,DHRS4L2,ECHDC2,EDF1,ENDOG,FKBP2,
GSTZ1,LOC440957,MRPL41,REEP6,TEX264,TUSC2,UQCRC1
ACAA1,ACSF2,RBFA,CHMP2A,DHRS4,DHRS4L2,ILVBL,
KLHL22,LOC729991,LONP1,LRPAP1,PEX10,PFKL,RAB1B,
SCYL1,SDF4,SIL1,SNF8,SPR,TOLLIP,UBXN6

ACAA1,ACY1,AIM1L,APEH,ARPC4,ATPIF1,CCDC12,
COMTD1,GIPC1,LYPLA2,LYPLA2P1,MRPS25,PKP3,SLC22A18,
SLC22A18AS,TALDO1,TMEM54,TUSC2,UQCRC1,VAMP8,ZDHHC3
ACAA1,C1orf106,C2CD2L,CLRN3,FTH1,FTH1P3,GCOM1,
HECTD3,HTATIP2,KCNK5,PLEKHG6,PRKCD,PRR13,RIOK3,
SDCBP2,SPINT1,SPINT2,SULT1A2,TUBAL3,VILL,ZNF57
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 ACAA1
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
DB02713acetyl-CoA acyltransferase 1experimentalAcetylamino-Acetic Acid
DB03085acetyl-CoA acyltransferase 1experimentalHydroxyacetic Acid
DB03147acetyl-CoA acyltransferase 1experimentalFlavin-Adenine Dinucleotide


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Cross referenced IDs for ACAA1
* 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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