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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for ACSM3 |
Basic gene info. | Gene symbol | ACSM3 |
Gene name | acyl-CoA synthetase medium-chain family member 3 | |
Synonyms | SA|SAH | |
Cytomap | UCSC genome browser: 16p13.11 | |
Genomic location | chr16 :20775311-20797638 | |
Type of gene | protein-coding | |
RefGenes | NM_005622.3, NM_202000.2, | |
Ensembl id | ENSG00000005187 | |
Description | SA (rat hypertension-associated) homologSA hypertension-associated homologacyl-coenzyme A synthetase ACSM3, mitochondrialbutyrate--CoA ligase 3butyryl-coenzyme A synthetase 3middle-chain acyl-CoA synthetase 3protein SA homolog | |
Modification date | 20141207 | |
dbXrefs | MIM : 145505 | |
HGNC : HGNC | ||
Ensembl : ENSG00000005187 | ||
HPRD : 07033 | ||
Vega : OTTHUMG00000131552 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_ACSM3 | |
BioGPS: 6296 | ||
Gene Expression Atlas: ENSG00000005187 | ||
The Human Protein Atlas: ENSG00000005187 | ||
Pathway | NCI Pathway Interaction Database: ACSM3 | |
KEGG: ACSM3 | ||
REACTOME: ACSM3 | ||
ConsensusPathDB | ||
Pathway Commons: ACSM3 | ||
Metabolism | MetaCyc: ACSM3 | |
HUMANCyc: ACSM3 | ||
Regulation | Ensembl's Regulation: ENSG00000005187 | |
miRBase: chr16 :20,775,311-20,797,638 | ||
TargetScan: NM_005622 | ||
cisRED: ENSG00000005187 | ||
Context | iHOP: ACSM3 | |
cancer metabolism search in PubMed: ACSM3 | ||
UCL Cancer Institute: ACSM3 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for ACSM3(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: ACSM3 |
Familial Cancer Database: ACSM3 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
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KEGG_BUTANOATE_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: ACSM3 |
MedGen: ACSM3 (Human Medical Genetics with Condition) | |
ClinVar: ACSM3 | |
Phenotype | MGI: ACSM3 (International Mouse Phenotyping Consortium) |
PhenomicDB: ACSM3 |
Mutations for ACSM3 |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ACSM3 related fusion information. |
ID | 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 |
BQ316181 | MLH3 | 27 | 416 | 14 | 75483703 | 75485719 | ACSM3 | 411 | 641 | 16 | 20792103 | 20792449 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=66) | (# total SNVs=13) |
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(# total SNVs=1) | (# total SNVs=1) |
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* 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 |
chr16:20803451-20803451 | p.G485V | 13 |
chr16:20793081-20793081 | p.R331* | 3 |
chr16:20796428-20796428 | p.T381M | 3 |
chr16:20803563-20803563 | p.R487Q | 3 |
chr16:20781479-20781479 | p.S41S | 3 |
chr16:20781555-20781555 | p.Q67* | 2 |
chr16:20781559-20781559 | p.W68* | 2 |
chr16:20796405-20796405 | p.Y373Y | 2 |
chr16:20792168-20792168 | p.S257S | 2 |
chr16:20803392-20803392 | p.M465I | 2 |
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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 | 1 | 1 |   | 8 | 1 |   | 4 |   | 2 | 1 |   | 4 | 4 | 2 |   |   | 7 | 4 |   | 13 |
# mutation | 1 | 1 |   | 7 | 1 |   | 4 |   | 2 | 1 |   | 5 | 4 | 2 |   |   | 7 | 4 |   | 17 |
nonsynonymous SNV |   | 1 |   | 5 | 1 |   | 1 |   | 2 |   |   | 4 | 4 | 1 |   |   | 7 | 3 |   | 15 |
synonymous SNV | 1 |   |   | 2 |   |   | 3 |   |   | 1 |   | 1 |   | 1 |   |   |   | 1 |   | 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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* 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 |
chr16:20781479 | p.S41S,ACSM3 | 3 |
chr16:20796428 | p.R487Q | 2 |
chr16:20803563 | p.T381M,ACSM3 | 2 |
chr16:20807792 | p.C349G,ACSM3 | 1 |
chr16:20788733 | p.A475A | 1 |
chr16:20796340 | p.R88I,ACSM3 | 1 |
chr16:20803376 | p.A352S,ACSM3 | 1 |
chr16:20781555 | p.D479N | 1 |
chr16:20807798 | p.R94R,ACSM3 | 1 |
chr16:20788787 | p.I356T,ACSM3 | 1 |
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* 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. |
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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 ACSM3 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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ACSM3,ADH1C,AFF2,AKR1B15,CHRNA2,EML5,EYS, GNAL,ISX,IYD,KLRF1,KPNA7,LOC255167,ME1, PLD5,RLN3,SC5D,SPINK8,SRD5A1,VSX2,WDR64 | ABCC11,ABCC2,ACSM3,AFMID,AKR1D1,B3GAT1,C6orf223, CHRNA2,CHST1,CLDN14,GSTT2,HMGCR,INSM2,LOC255167, OR4N4,RIMS1,SLC5A11,SLCO1B1,SYCP1,TRPC7,ZP2 |
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ACSM1,ACSM3,CRYM,GNG13,HTR3C,HTR3E,LOC100189589, NPY6R,NXF3,OR2T34,PRH1,PRH2,RGS13,RGS21, SH2D6,SH2D7,TAS1R1,TAS1R2,TCL6,THUMPD1,USP26 | ACSM3,BSPRY,HMGN2P46,CDC25C,CEP70,CNOT10,COX5A, EHF,ERLIN1,FRAT2,MLEC,MTIF2,MYB,RTN4IP1, SCO1,STARD7,STIL,TAF5,TRIM34,WIPI1,ZNF695 |
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* 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 |
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Pharmacological Information for ACSM3 |
There's no related Drug. |
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Cross referenced IDs for ACSM3 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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