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 ACSM4
Basic gene info.Gene symbolACSM4
Gene nameacyl-CoA synthetase medium-chain family member 4
Synonyms-
CytomapUCSC genome browser: 12p13.31
Genomic locationchr12 :7456927-7480969
Type of geneprotein-coding
RefGenesNM_001080454.1,
Ensembl idENSG00000215009
Descriptionacyl-coenzyme A synthetase ACSM4, mitochondrial
Modification date20141207
dbXrefs MIM : 614360
HGNC : HGNC
Ensembl : ENSG00000215009
Vega : OTTHUMG00000154975
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACSM4
BioGPS: 341392
Gene Expression Atlas: ENSG00000215009
The Human Protein Atlas: ENSG00000215009
PathwayNCI Pathway Interaction Database: ACSM4
KEGG: ACSM4
REACTOME: ACSM4
ConsensusPathDB
Pathway Commons: ACSM4
MetabolismMetaCyc: ACSM4
HUMANCyc: ACSM4
RegulationEnsembl's Regulation: ENSG00000215009
miRBase: chr12 :7,456,927-7,480,969
TargetScan: NM_001080454
cisRED: ENSG00000215009
ContextiHOP: ACSM4
cancer metabolism search in PubMed: ACSM4
UCL Cancer Institute: ACSM4
Assigned class in ccmGDBC

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Phenotypic Information for ACSM4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACSM4
Familial Cancer Database: ACSM4
* 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: ACSM4
MedGen: ACSM4 (Human Medical Genetics with Condition)
ClinVar: ACSM4
PhenotypeMGI: ACSM4 (International Mouse Phenotyping Consortium)
PhenomicDB: ACSM4

Mutations for ACSM4
* 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
breastACSM4chr1274735327473532chr1274978277497827
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 ACSM4 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 # sample2                
GAIN (# sample)2                
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=57)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr12:7470689-7470689p.A278S3
chr12:7473381-7473381p.V328L2
chr12:7470723-7470723p.G289E2
chr12:7479625-7479625p.E530D2
chr12:7475888-7475888p.G395E2
chr12:7476100-7476100p.E418K2
chr12:7459281-7459281p.A118A2
chr12:7456958-7456958p.R11G2
chr12:7477189-7477189p.G511R1
chr12:7459299-7459299p.I124I1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 75 2 1  3103  205 9
# mutation13 105 2 1  3103  245 11
nonsynonymous SNV 2 65      281  165 9
synonymous SNV11 4  2 1  122  8  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
chr12:7476100p.G395E2
chr12:7469736p.E418K2
chr12:7475888p.F208F2
chr12:7475910p.G138G1
chr12:7463195p.C253C1
chr12:7469871p.G376R1
chr12:7477186p.R510C1
chr12:7457003p.D26N1
chr12:7475033p.I140I1
chr12:7459281p.I265M1

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 ACSM4 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 ACSM4

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

ACSM4,ADAM17,ARNTL2,ASUN,C12orf4,MB21D1,CD163L1,
DSC2,DSG1,FAM135A,GOLT1B,WNK1,LOC143188,MSL3P1,
PSME4,R3HDM1,SAA3P,ZNF254,ZNF280C,ZNF675,ZNF681
ACSM4,ARR3,C10orf113,C1orf146,LINC00320,C4orf17,CA10,
CST11,DCAF8L2,GAGE10,KCNK18,LCE3D,OR51F1,SCGB1D2,
SLC17A1,SNORA11D,SNORA11E,SNORA77,SNORD22,SPAG11A,TSPAN16

ACSM4,LINC01551,GOLGA6D,GPR149,GPR61,GRIN1,LCE5A,
LIM2,OR10C1,OR10J1,OR6C70,OR6F1,OR9Q1,PRTN3,
RBM44,RPL13AP17,SLC39A12,SLC6A7,TKTL2,TMEM145,UBE2DNL
ACSM4,BANK1,BTLA,CCDC155,CD19,CD37,CLEC17A,
CNR2,CXCL13,GAPT,HSF5,LOC283663,LTF,MAGEA2,
MAP4K2,PARP15,STK4,TNFRSF13C,TTC24,TUBB7P,VPREB3
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 ACSM4


There's no related Drug.
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Cross referenced IDs for ACSM4
* 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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