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 ACSS3
Basic gene info.Gene symbolACSS3
Gene nameacyl-CoA synthetase short-chain family member 3
Synonyms-
CytomapUCSC genome browser: 12q21.31
Genomic locationchr12 :81471808-81649582
Type of geneprotein-coding
RefGenesNM_024560.2,
Ensembl idENSG00000111058
DescriptionAMP-binding enzyme, 33217acyl-CoA synthetase short-chain family member 3, mitochondrial
Modification date20141207
dbXrefs MIM : 614356
HGNC : HGNC
Ensembl : ENSG00000111058
HPRD : 13385
Vega : OTTHUMG00000170179
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACSS3
BioGPS: 79611
Gene Expression Atlas: ENSG00000111058
The Human Protein Atlas: ENSG00000111058
PathwayNCI Pathway Interaction Database: ACSS3
KEGG: ACSS3
REACTOME: ACSS3
ConsensusPathDB
Pathway Commons: ACSS3
MetabolismMetaCyc: ACSS3
HUMANCyc: ACSS3
RegulationEnsembl's Regulation: ENSG00000111058
miRBase: chr12 :81,471,808-81,649,582
TargetScan: NM_024560
cisRED: ENSG00000111058
ContextiHOP: ACSS3
cancer metabolism search in PubMed: ACSS3
UCL Cancer Institute: ACSS3
Assigned class in ccmGDBC

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Phenotypic Information for ACSS3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACSS3
Familial Cancer Database: ACSS3
* 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_PROPANOATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACSS3
MedGen: ACSS3 (Human Medical Genetics with Condition)
ClinVar: ACSS3
PhenotypeMGI: ACSS3 (International Mouse Phenotyping Consortium)
PhenomicDB: ACSS3

Mutations for ACSS3
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
breastACSS3chr128158784581588245CEP112chr176394817863948578
pancreasACSS3chr128147939181479411PKP2chr123295282932952849
pancreasACSS3chr128148998381490003chr128584640985846429
pancreasACSS3chr128149051181490531ACSS3chr128149083681490856
pancreasACSS3chr128150794381507963chr128143151481431534
pancreasACSS3chr128152741381527433chr123406779034067810
pancreasACSS3chr128159652581596545PPFIA2chr128167835181678371
pancreasACSS3chr128160345681603476ACSS3chr128159639681596416
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 ACSS3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI871518SMARCD21332176190944461909772ACSS3317337128161275481612774

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 # sample11   1       11  
GAIN (# sample)11   1       11  
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=89)
Stat. for Synonymous SNVs
(# total SNVs=25)
Stat. for Deletions
(# total SNVs=3)
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
chr12:81647354-81647354p.R634*4
chr12:81536974-81536974p.S290L3
chr12:81536902-81536902p.A266V3
chr12:81471976-81471976p.P26L2
chr12:81648681-81648681p.E681*2
chr12:81503375-81503375p.A116A2
chr12:81545790-81545790p.A338E2
chr12:81503376-81503376p.V117I2
chr12:81647408-81647408p.R652G2
chr12:81624915-81624915p.P532S2

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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
# sample54 13  11 1 11281  246 8
# mutation54 13  10 1 11481  357 9
nonsynonymous SNV33 8  7 1 187   276 8
synonymous SNV21 5  3    611  81 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
chr12:81532986p.A241E2
chr12:81503375p.E452E2
chr12:81610681p.R634Q2
chr12:81537007p.A459V2
chr12:81627142p.R269C2
chr12:81610701p.G579C2
chr12:81647355p.A116A2
chr12:81647101p.T537T2
chr12:81536910p.G301V2
chr12:81471976p.D539H1

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 ACSS3 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 ACSS3

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

ACSF2,ACSM1,ACSS3,ALCAM,ALOX15B,ARFGEF2,C15orf43,
CHRNA2,HERC3,ISX,LIN7A,MPV17L,PXMP4,SAR1B,
SCP2,SULT1C3,TMEM86A,TMIGD1,TRIM68,UGT2B28,ZNF652
ABHD15,ACACB,ACSS3,ACVR1C,ADH1A,ADH1B,ALDH6A1,
BNIP3L,GPATCH11,RHOV___CHP1,EIF4EBP2,EPB41L4B,EYS,GHR,
GNAI1,GYG2,LOC283392,PCCA,PDP2,PECR,SLC19A3

ACSS3,ASPA,CAGE1,CCDC67,CNN3,DYNC1I1,KCNC2,
KLRF1,LGALS13,LOC100129935,ODF2L,OLAH,OR6F1,OR7E156P,
PCDH8,PLAC4,RNF113B,SLC22A1,SNAR-B2,SNAR-I,TRIM63
ABCC9,ACSS3,ATP2B3,BHLHB9,BOC,CNGA3,CPEB1,
DIXDC1,DMGDH,SUPT20HL2,FBXL22,HLF,KCNJ8,LGI2,
LOXL4,PDE2A,PHGDH,RGS4,RHOJ,SALL2,SEMA4C
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 ACSS3


There's no related Drug.
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Cross referenced IDs for ACSS3
* 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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