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 ACSM5
Basic gene info.Gene symbolACSM5
Gene nameacyl-CoA synthetase medium-chain family member 5
Synonyms-
CytomapUCSC genome browser: 16p12.3
Genomic locationchr16 :20420855-20452281
Type of geneprotein-coding
RefGenesNM_017888.2,
Ensembl idENSG00000183549
Descriptionacyl-coenzyme A synthetase ACSM5, mitochondrial
Modification date20141211
dbXrefs MIM : 614361
HGNC : HGNC
Ensembl : ENSG00000183549
HPRD : 08627
Vega : OTTHUMG00000131551
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACSM5
BioGPS: 54988
Gene Expression Atlas: ENSG00000183549
The Human Protein Atlas: ENSG00000183549
PathwayNCI Pathway Interaction Database: ACSM5
KEGG: ACSM5
REACTOME: ACSM5
ConsensusPathDB
Pathway Commons: ACSM5
MetabolismMetaCyc: ACSM5
HUMANCyc: ACSM5
RegulationEnsembl's Regulation: ENSG00000183549
miRBase: chr16 :20,420,855-20,452,281
TargetScan: NM_017888
cisRED: ENSG00000183549
ContextiHOP: ACSM5
cancer metabolism search in PubMed: ACSM5
UCL Cancer Institute: ACSM5
Assigned class in ccmGDBC

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Phenotypic Information for ACSM5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACSM5
Familial Cancer Database: ACSM5
* 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_BUTANOATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ACSM5
MedGen: ACSM5 (Human Medical Genetics with Condition)
ClinVar: ACSM5
PhenotypeMGI: ACSM5 (International Mouse Phenotyping Consortium)
PhenomicDB: ACSM5

Mutations for ACSM5
* 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 ACSM5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample1                
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=80)
Stat. for Synonymous SNVs
(# total SNVs=29)
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
chr16:20442562-20442562p.N409N4
chr16:20442608-20442608p.P425T3
chr16:20442613-20442613p.T426T3
chr16:20442344-20442344p.M385I3
chr16:20429402-20429402p.P76S2
chr16:20422911-20422911p.I35I2
chr16:20429440-20429440p.I88I2
chr16:20442387-20442387p.D400N2
chr16:20439127-20439127p.P313P2
chr16:20451726-20451726p.R573*2

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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
# sample13 82 8 1  27112  21219
# mutation13 82 8 1  27113  25219
nonsynonymous SNV12 61 5 1  1663  14117
synonymous SNV 1 21 3    115   111 2
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
chr16:20422911p.P76T2
chr16:20448643p.R422H2
chr16:20429402p.V497A2
chr16:20442600p.I35I2
chr16:20435240p.E182D1
chr16:20442617p.I266I1
chr16:20439149p.P352P1
chr16:20448599p.D449N1
chr16:20429585p.I509M1
chr16:20430747p.S43R1

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 ACSM5 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 ACSM5

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

ACSM5,ADH1A,ADH1B,ADIPOQ,AOC3,AQP7,AQP7P1,
AQPEP,C14orf180,CHRDL1,CIDEC,CRHBP,GPD1,HEPACAM,
KCNIP2,LIPE,PLIN1,PLIN4,SLC19A3,TMEM132C,TMEM37
ABHD15,ACO1,ACSM5,ALDH2,AOC3,AQP7,FAM213A,
CIDEC,CPM,FAH,FBXO27,GYG2,HEPACAM,MAOA,
PLA2G16,PLIN1,RDH5,RHOBTB3,SH3KBP1,TMEM132C,TYRO3

ACSM5,ADH1B,ADIPOQ,CD300LG,CD36,EPB42,FABP4,
FMO2,GLYAT,HEPACAM,LBP,LEP,LIPE,LOC339524,
MRAP,PLIN4,PTCHD3,SCN4A,SEMA3G,SGCG,TUSC5
ACSM5,CCDC144NL,CD300LG,CHRDL2,CNBD1,DEFB124,DYDC1,
FAP,FOLR2,GGTA1P,GLYCAM1,IMPG2,KCNJ5,LIM2,
MARCO,OR3A4P,RBP7,SBSN,SCN4A,SNORA22,TSPAN4
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 ACSM5


There's no related Drug.
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Cross referenced IDs for ACSM5
* 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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