Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	ACSS3
	Gene name	acyl-CoA synthetase short-chain family member 3
	Synonyms	-
	Cytomap	UCSC genome browser: 12q21.31
	Genomic location	chr12 :81471808-81649582
	Type of gene	protein-coding
	RefGenes	NM_024560.2,
	Ensembl id	ENSG00000111058
	Description	AMP-binding enzyme, 33217acyl-CoA synthetase short-chain family member 3, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 614356
	HGNC : HGNC
	Ensembl : ENSG00000111058
	HPRD : 13385
	Vega : OTTHUMG00000170179
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ACSS3
	BioGPS: 79611
	Gene Expression Atlas: ENSG00000111058
	The Human Protein Atlas: ENSG00000111058
Pathway	NCI Pathway Interaction Database: ACSS3
	KEGG: ACSS3
	REACTOME: ACSS3
	ConsensusPathDB
	Pathway Commons: ACSS3
Metabolism	MetaCyc: ACSS3
	HUMANCyc: ACSS3
Regulation	Ensembl's Regulation: ENSG00000111058
	miRBase: chr12 :81,471,808-81,649,582
	TargetScan: NM_024560
	cisRED: ENSG00000111058
Context	iHOP: ACSS3
	cancer metabolism search in PubMed: ACSS3
	UCL Cancer Institute: ACSS3
Assigned class in ccmGDB	C

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Phenotypic Information for ACSS3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_PROPANOATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: ACSS3
	MedGen: ACSS3 (Human Medical Genetics with Condition)
	ClinVar: ACSS3
Phenotype	MGI: ACSS3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	ACSS3	chr12	81587845	81588245	CEP112	chr17	63948178	63948578
pancreas	ACSS3	chr12	81479391	81479411	PKP2	chr12	32952829	32952849
pancreas	ACSS3	chr12	81489983	81490003		chr12	85846409	85846429
pancreas	ACSS3	chr12	81490511	81490531	ACSS3	chr12	81490836	81490856
pancreas	ACSS3	chr12	81507943	81507963		chr12	81431514	81431534
pancreas	ACSS3	chr12	81527413	81527433		chr12	34067790	34067810
pancreas	ACSS3	chr12	81596525	81596545	PPFIA2	chr12	81678351	81678371
pancreas	ACSS3	chr12	81603456	81603476	ACSS3	chr12	81596396	81596416

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ACSS3 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

AI871518

SMARCD2

332

61909444

61909772

ACSS3

317

337

81612754

81612774

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr12:81647354-81647354	p.R634*	4
chr12:81536974-81536974	p.S290L	3
chr12:81536902-81536902	p.A266V	3
chr12:81537028-81537028	p.?	2
chr12:81624915-81624915	p.P532S	2
chr12:81503382-81503382	p.R119C	2
chr12:81627231-81627231	p.S567Y	2
chr12:81536910-81536910	p.R269C	2
chr12:81610767-81610767	p.G481E	2
chr12:81627233-81627233	p.A568S	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	5	4		13			11		1		1	12	8	1			24	6		8
# mutation	5	4		13			10		1		1	14	8	1			35	7		9
nonsynonymous SNV	3	3		8			7		1		1	8	7				27	6		8
synonymous SNV	2	1		5			3					6	1	1			8	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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr12:81536910	p.R269C	2
chr12:81532986	p.G579C	2
chr12:81503375	p.A116A	2
chr12:81610681	p.G301V	2
chr12:81537007	p.T537T	2
chr12:81627142	p.A241E	2
chr12:81610701	p.E452E	2
chr12:81647355	p.A459V	2
chr12:81647101	p.R634Q	2
chr12:81533033	p.E681K	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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