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 ACAA2
Basic gene info.Gene symbolACAA2
Gene nameacetyl-CoA acyltransferase 2
SynonymsDSAEC
CytomapUCSC genome browser: 18q21.1
Genomic locationchr18 :47309873-47340251
Type of geneprotein-coding
RefGenesNM_006111.2,
Ensembl idENSG00000167315
Description3-ketoacyl-CoA thiolase, mitochondrialT1acetyl-Coenzyme A acyltransferase 2beta ketothiolasebeta-ketothiolasemitochondrial 3-oxoacyl-CoA thiolasemitochondrial 3-oxoacyl-Coenzyme A thiolase
Modification date20141207
dbXrefs MIM : 604770
HGNC : HGNC
HPRD : 10380
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACAA2
BioGPS: 10449
Gene Expression Atlas: ENSG00000167315
The Human Protein Atlas: ENSG00000167315
PathwayNCI Pathway Interaction Database: ACAA2
KEGG: ACAA2
REACTOME: ACAA2
ConsensusPathDB
Pathway Commons: ACAA2
MetabolismMetaCyc: ACAA2
HUMANCyc: ACAA2
RegulationEnsembl's Regulation: ENSG00000167315
miRBase: chr18 :47,309,873-47,340,251
TargetScan: NM_006111
cisRED: ENSG00000167315
ContextiHOP: ACAA2
cancer metabolism search in PubMed: ACAA2
UCL Cancer Institute: ACAA2
Assigned class in ccmGDBC

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Phenotypic Information for ACAA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACAA2
Familial Cancer Database: ACAA2
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACAA2
MedGen: ACAA2 (Human Medical Genetics with Condition)
ClinVar: ACAA2
PhenotypeMGI: ACAA2 (International Mouse Phenotyping Consortium)
PhenomicDB: ACAA2

Mutations for ACAA2
* 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
ovaryACAA2chr184733730547337325STARD6chr185186878951868809
pancreasACAA2chr184733730547337325STARD6chr185186878451868804
pancreasACAA2chr184733730547337325STARD6chr185186878951868809
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 ACAA2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE842124ACAA213144184731370247317942SMG1137409161884561518846340
BQ328229MAML1183025179202226179202513ACAA2294650184731006947311692
DA908810CXorf381353X4050625940506774ACAA2352555184732217947323966
AV688387ACAA21438184732217647339910LOC1005059894274494165698716165698741

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 # sample      1          
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=28)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr18:47310298-47310298p.R371R3
chr18:47310299-47310299p.R371H2
chr18:47320663-47320663p.Q188H2
chr18:47320707-47320707p.I174V2
chr18:47317852-47317852p.I291V2
chr18:47322226-47322226p.V113A1
chr18:47329086-47329086p.D52Y1
chr18:47317897-47317897p.L276L1
chr18:47322241-47322241p.V108A1
chr18:47329179-47329179p.G21*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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 8  1    311  54 3
# mutation12 6  1    311  54 3
nonsynonymous SNV12 4  1    211  23 3
synonymous SNV   2       1    31  
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
chr18:47310298p.R371R3
chr18:47310300p.R371C2
chr18:47323960p.S98P1
chr18:47310299p.E368K1
chr18:47320717p.Q97E1
chr18:47329069p.V343M1
chr18:47320775p.R76C1
chr18:47329180p.Q326R1
chr18:47311574p.H72D1
chr18:47322138p.P325S1

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 ACAA2 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 ACAA2

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

ACAA2,ATP5A1,TPGS2,TIMM21,CCNJ,DSC2,DYM,
FAM171A1,HDAC2,KDM1A,KIF3C,ME2,MEX3A,MEX3C,
MTHFD1L,SKA1,SMAD2,STMN1,TUBA1A,TXNL1,ZC4H2
ABHD15,ACAA2,ACACB,ACO1,ACOT1,ALDH2,AQP7,
AQPEP,CIDEC,GBE1,GYG2,KCNIP2,MARC1,PECR,
PEX19,PFKFB1,PLA2G16,PNPLA2,PPARG,PPP1R1A,PRDX6

ACAA2,ATP5A1,ATPAF2,C15orf48,LRRC75A,CLDN7,EHD4,
FAM118B,GDE1,GGT6,LGALS3,MYO5B,OVCA2,PAFAH2,
PPP1R14D,RHOC,RILP,SULT1B1,TAX1BP3,TMEM144,TXNL1
ACAA2,BCAS4,LINC00483,STPG1,CASP7,RHOV___CHP1,MARVELD3,
MYL12A,PAPSS2,PKIB,PLAC8,PPP1R14D,RAB9A,RAC1,
SFXN1,SPPL2A,TJP3,TMEM45B,TNK1,TPRN,TRIP4
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 ACAA2


There's no related Drug.
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Cross referenced IDs for ACAA2
* 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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