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 ACAT2
Basic gene info.Gene symbolACAT2
Gene nameacetyl-CoA acetyltransferase 2
Synonyms-
CytomapUCSC genome browser: 6q25.3
Genomic locationchr6 :160182988-160200087
Type of geneprotein-coding
RefGenesNM_005891.2,
Ensembl idENSG00000120437
Descriptionacetoacetyl Coenzyme A thiolaseacetyl-CoA acetyltransferase, cytosolicacetyl-CoA transferase-like proteincytosolic acetoacetyl-CoA thiolase
Modification date20141207
dbXrefs MIM : 100678
HGNC : HGNC
HPRD : 00006
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACAT2
BioGPS: 39
Gene Expression Atlas: ENSG00000120437
The Human Protein Atlas: ENSG00000120437
PathwayNCI Pathway Interaction Database: ACAT2
KEGG: ACAT2
REACTOME: ACAT2
ConsensusPathDB
Pathway Commons: ACAT2
MetabolismMetaCyc: ACAT2
HUMANCyc: ACAT2
RegulationEnsembl's Regulation: ENSG00000120437
miRBase: chr6 :160,182,988-160,200,087
TargetScan: NM_005891
cisRED: ENSG00000120437
ContextiHOP: ACAT2
cancer metabolism search in PubMed: ACAT2
UCL Cancer Institute: ACAT2
Assigned class in ccmGDBC

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Phenotypic Information for ACAT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACAT2
Familial Cancer Database: ACAT2
* 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
KEGG_TRYPTOPHAN_METABOLISM
KEGG_PYRUVATE_METABOLISM
KEGG_PROPANOATE_METABOLISM
KEGG_BUTANOATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACAT2
MedGen: ACAT2 (Human Medical Genetics with Condition)
ClinVar: ACAT2
PhenotypeMGI: ACAT2 (International Mouse Phenotyping Consortium)
PhenomicDB: ACAT2

Mutations for ACAT2
* 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 ACAT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE893428TCP19976160200926160201014ACAT2926796160199894160200946
BG766524ACAT222086160198374160199294ACAT22063796160199530160199703

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)                 
LOSS (# sample)   1             
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=2)
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
chr6:160189651-160189651p.G161S4
chr6:160199295-160199295p.G336R2
chr6:160183126-160183126p.A3S2
chr6:160189609-160189609p.L147I2
chr6:160198395-160198395p.G273G2
chr6:160199311-160199311p.K341R2
chr6:160199689-160199689p.?1
chr6:160183182-160183182p.?1
chr6:160198412-160198412p.R279Q1
chr6:160199754-160199754p.L363I1

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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
# sample 2 7  2    211  14 3
# mutation 2 5  2    211  14 4
nonsynonymous SNV   5  1    1 1  14 4
synonymous SNV 2    1    11       
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
chr6:160189651p.G161S3
chr6:160188084p.S282S1
chr6:160198422p.I292V1
chr6:160188151p.A329S1
chr6:160198450p.A330A1
chr6:160189602p.N22S1
chr6:160199274p.L335V1
chr6:160189620p.P49L1
chr6:160199279p.P80S1
chr6:160199292p.G347G1

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 ACAT2 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 ACAT2

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

ACAT2,CCNB2,CDC45,CENPN,CHEK1,DLGAP5,DONSON,
MTFR2,FBXO5,FDPS,KIF20A,KIF23,KIF4A,MRPL18,
NCAPG,NCAPH,NDC80,OIP5,TCP1,TTK,TUBB
AACS,ACAT2,ACP6,AKR1A1,ALDH3B2,DBI,DHCR7,
EBP,ENPP3,FDFT1,FDPS,GGT1,GGTLC2,HGD,
HIST1H3D,IVD,MMAB,MVD,MVK,QPRT,SLC50A1

ACAT2,C14orf1,CYP51A1,DBI,DHCR24,DHCR7,FDPS,
HMGCR,HMGCS1,HSD17B7,IDH1,IDI1,INSIG1,LSS,
MTCH2,MVD,MVK,PCSK9,MSMO1,SC5D,SQLE
AAGAB,ACAT2,ACTR3,C20orf24,CASP5,CCNE2,DBI,
FDFT1,FDPS,IDI1,LOC541471,PNP,PSMC4,PSMD3,
RAB11A,RAB1A,RP2,STX12,TCP1,TOR3A,UEVLD
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 ACAT2
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
DB01915acetyl-CoA acetyltransferase 2experimentalS-Hydroxycysteine
DB01992acetyl-CoA acetyltransferase 2experimentalCoenzyme A
DB00363acetyl-CoA acetyltransferase 2approvedClozapine


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Cross referenced IDs for ACAT2
* 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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