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 ACAT1
Basic gene info.Gene symbolACAT1
Gene nameacetyl-CoA acetyltransferase 1
SynonymsACAT|MAT|T2|THIL
CytomapUCSC genome browser: 11q22.3
Genomic locationchr11 :107992257-108018891
Type of geneprotein-coding
RefGenesNM_000019.3,
Ensembl idENSG00000075239
Descriptionacetoacetyl Coenzyme A thiolaseacetoacetyl-CoA thiolaseacetyl-CoA acetyltransferase, mitochondrialacetyl-Coenzyme A acetyltransferase 1mitochondrial acetoacetyl-CoA thiolase
Modification date20141207
dbXrefs MIM : 607809
HGNC : HGNC
Ensembl : ENSG00000075239
HPRD : 01946
Vega : OTTHUMG00000166381
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACAT1
BioGPS: 38
Gene Expression Atlas: ENSG00000075239
The Human Protein Atlas: ENSG00000075239
PathwayNCI Pathway Interaction Database: ACAT1
KEGG: ACAT1
REACTOME: ACAT1
ConsensusPathDB
Pathway Commons: ACAT1
MetabolismMetaCyc: ACAT1
HUMANCyc: ACAT1
RegulationEnsembl's Regulation: ENSG00000075239
miRBase: chr11 :107,992,257-108,018,891
TargetScan: NM_000019
cisRED: ENSG00000075239
ContextiHOP: ACAT1
cancer metabolism search in PubMed: ACAT1
UCL Cancer Institute: ACAT1
Assigned class in ccmGDBC

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Phenotypic Information for ACAT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACAT1
Familial Cancer Database: ACAT1
* 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
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACAT1
MedGen: ACAT1 (Human Medical Genetics with Condition)
ClinVar: ACAT1
PhenotypeMGI: ACAT1 (International Mouse Phenotyping Consortium)
PhenomicDB: ACAT1

Mutations for ACAT1
* 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
ovaryACAT1chr11108004471108004491ACAT1chr11107999069107999089
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 ACAT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK024206ACAT1174811108007716108008511VPRBP74376235149676151496780

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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr11:107992346-107992346p.A5P5
chr11:108017059-108017059p.G379A2
chr11:108009660-108009660p.S157S2
chr11:108017053-108017053p.N377T1
chr11:108004595-108004595p.G57C1
chr11:108009666-108009666p.V159V1
chr11:108012384-108012384p.F261F1
chr11:108004653-108004653p.I76N1
chr11:108009744-108009744p.T185T1
chr11:108013182-108013182p.N282S1

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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
# sample12 6      1 22 1 3 4
# mutation12 7      1 23 1 3 6
nonsynonymous SNV 2 4        22 1 3 5
synonymous SNV1  3      1  1     1
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
chr11:108005922p.Y407C1
chr11:108012384p.S139G1
chr11:108005924p.S139N1
chr11:108013239p.S139S1
chr11:108005949p.V159V1
chr11:108014720p.T185T1
chr11:108005950p.H192N1
chr11:108017007p.D212D1
chr11:108002641p.R27I1
chr11:108005951p.T239A1

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 ACAT1 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 ACAT1

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

ACAT1,ALG9,ALKBH8,ARCN1,C11orf1,C11orf52,C11orf57,
CUL5,DDX10,DLAT,DPAGT1,EI24,IFT46,KBTBD3,
NLRX1,ECI2,PPP2R1B,SIAE,TMEM25,TRAPPC4,VPS11
ACAT1,ACO2,ATP5B,ATPAF1,CHCHD3,ETFDH,HADHB,
HOXA10,HSPB6,NRD1,OPTN,PGM1,PHYH,RRAGD,
SDHB,SGCG,SLC2A4,SNTA1,ST3GAL3,SUCLA2,TBX15

ACADSB,ACAT1,BOLA3,CHCHD4,COQ3,COQ9,DLAT,
FASTKD1,FH,HSPA9,HSPD1,IMMT,LRPPRC,MRPL16,
MTCH2,NDUFAF4,NDUFV1,NLN,PDHA1,SDHD,SUPV3L1
ACAA2,ACAT1,BSG,BTBD3,CA2,CD24,CPT2,
ETHE1,GHITM,LCMT1,PGM1,PKIB,PPARG,SDHA,
SLC16A1,TMEM171,TSPAN7,TST,UBE2D2,UGT1A10,WDR78
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 ACAT1
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
DB00795acetyl-CoA acetyltransferase 1approvedSulfasalazine


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Cross referenced IDs for ACAT1
* 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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