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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for ACADM |
Basic gene info. | Gene symbol | ACADM |
Gene name | acyl-CoA dehydrogenase, C-4 to C-12 straight chain | |
Synonyms | ACAD1|MCAD|MCADH | |
Cytomap | UCSC genome browser: 1p31 | |
Genomic location | chr1 :76190042-76229355 | |
Type of gene | protein-coding | |
RefGenes | NM_000016.5, NM_001127328.2,NM_001286042.1,NM_001286043.1,NM_001286044.1, NR_022013.1, | |
Ensembl id | ENSG00000117054 | |
Description | acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chainmedium-chain specific acyl-CoA dehydrogenase, mitochondrial | |
Modification date | 20141222 | |
dbXrefs | MIM : 607008 | |
HGNC : HGNC | ||
Ensembl : ENSG00000117054 | ||
HPRD : 08447 | ||
Vega : OTTHUMG00000009784 | ||
Protein | UniProt: P11310 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_ACADM | |
BioGPS: 34 | ||
Gene Expression Atlas: ENSG00000117054 | ||
The Human Protein Atlas: ENSG00000117054 | ||
Pathway | NCI Pathway Interaction Database: ACADM | |
KEGG: ACADM | ||
REACTOME: ACADM | ||
ConsensusPathDB | ||
Pathway Commons: ACADM | ||
Metabolism | MetaCyc: ACADM | |
HUMANCyc: ACADM | ||
Regulation | Ensembl's Regulation: ENSG00000117054 | |
miRBase: chr1 :76,190,042-76,229,355 | ||
TargetScan: NM_000016 | ||
cisRED: ENSG00000117054 | ||
Context | iHOP: ACADM | |
cancer metabolism search in PubMed: ACADM | ||
UCL Cancer Institute: ACADM | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of ACADM in cancer cell metabolism | 1. Kelly TJ, Lerin C, Haas W, Gygi SP, Puigserver P (2009) GCN5-mediated transcriptional control of the metabolic coactivator PGC-1beta through lysine acetylation. J Biol Chem 284: 19945-19952. doi: 10.1074/jbc.M109.015164. pmid: 2740420 go to article 2. Wang F, Kumagai-Braesch M, Herrington MK, Larsson J, Permert J (2009) Increased lipid metabolism and cell turnover of MiaPaCa2 cells induced by high-fat diet in an orthotopic system. Metabolism 58: 1131-1136. doi: 10.1016/j.metabol.2009.03.027 go to article 3. Huang D, Li T, Li X, Zhang L, Sun L, et al. (2014) HIF-1-mediated suppression of acyl-CoA dehydrogenases and fatty acid oxidation is critical for cancer progression. Cell Rep 8: 1930-1942. doi: 10.1016/j.celrep.2014.08.028 go to article |
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Phenotypic Information for ACADM(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: ACADM |
Familial Cancer Database: ACADM |
* 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/ |
Metabolic Pathway Description | |
KEGG_FATTY_ACID_METABOLISM KEGG_BETA_ALANINE_METABOLISM KEGG_PROPANOATE_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | 201450; phenotype. 607008; gene. |
Orphanet | 42; Medium chain acyl-CoA dehydrogenase deficiency. |
Disease | KEGG Disease: ACADM |
MedGen: ACADM (Human Medical Genetics with Condition) | |
ClinVar: ACADM | |
Phenotype | MGI: ACADM (International Mouse Phenotyping Consortium) |
PhenomicDB: ACADM |
Mutations for ACADM |
* 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 | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | ACADM | chr1 | 76203682 | 76203702 | ACADM | chr1 | 76208012 | 76208032 |
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 ACADM 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 |
Other DBs for Structural Variants |
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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 | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=39) | (# total SNVs=10) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr1:76205781-76205781 | p.G195G | 3 |
chr1:76215151-76215151 | p.F252F | 3 |
chr1:76199306-76199306 | p.S127F | 3 |
chr1:76205779-76205779 | p.G195R | 3 |
chr1:76200483-76200483 | p.P132L | 2 |
chr1:76198353-76198353 | p.F48C | 2 |
chr1:76199293-76199293 | p.I123V | 2 |
chr1:76228408-76228408 | p.L409R | 1 |
chr1:76190487-76190487 | p.F5F | 1 |
chr1:76198547-76198547 | p.P76S | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   |   | 11 |   |   | 3 |   | 1 |   |   | 5 | 1 | 3 |   |   | 7 | 3 |   | 10 |
# mutation |   |   |   | 8 |   |   | 3 |   | 1 |   |   | 5 | 1 | 3 |   |   | 7 | 3 |   | 10 |
nonsynonymous SNV |   |   |   | 5 |   |   | 3 |   | 1 |   |   | 5 | 1 | 2 |   |   | 6 | 3 |   | 9 |
synonymous SNV |   |   |   | 3 |   |   |   |   |   |   |   |   |   | 1 |   |   | 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 |
chr1:76205781 | p.G6G,ACADM | 3 |
chr1:76215151 | p.F63F,ACADM | 3 |
chr1:76199306 | p.F12C,ACADM | 2 |
chr1:76198353 | p.S91Y,ACADM | 2 |
chr1:76205759 | p.F18L,ACADM | 1 |
chr1:76194104 | p.G130A,ACADM | 1 |
chr1:76215193 | p.G78E,ACADM | 1 |
chr1:76198595 | p.A27S,ACADM | 1 |
chr1:76205772 | p.D132N,ACADM | 1 |
chr1:76194107 | p.F120F,ACADM | 1 |
Other DBs for Point Mutations |
Copy Number for ACADM 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 ACADM |
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. |
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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 |
ACADM,AKR1D1,ANKRD13C,ATP13A4,CTBS,DBT,FKBP5, GUSB,IDI1,LOC91948,MIER1,MYOM2,PIGK,PKN2, PNPLA8,RNASE11,RNASE12,SC5D,SCP2,TYW3,USP33 | ACADM,ALPK3,ATP5B,CECR2,CRAT,DLD,MTFR1L, GHITM,HADHB,KLHL31,NDUFS1,NNT,NRD1,PARK2, PDHX,SAR1B,SIX1,SUCLA2,UBR3,UQCRFS1,ZYG11B | ||||
ABCD3,ACADM,AGL,ALDH6A1,ANKRD13C,ATG4C,ATP5F1, CPT2,CTBS,DBT,ETFDH,FPGT,MIER1,OMA1, PIGK,RPF1,RSBN1,SCP2,STXBP3,TMEM59,USP33 | ACADM,ATP6V0D2,AUH,BIRC2,C11orf71,PPP1R36,CAT, CHPT1,CRYL1,EAPP,FBXL3,CMTR2,GLUD2,GPR160, IPP,PECR,PHYH,PPP1CC,SNX14,TP53TG1,TSTD1 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for ACADM |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA24425; -. |
Organism-specific databases | CTD | 34; -. |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB02910 | acyl-CoA dehydrogenase, C-4 to C-12 straight chain | experimental | Octanoyl-Coenzyme A | ||
DB03147 | acyl-CoA dehydrogenase, C-4 to C-12 straight chain | experimental | Flavin-Adenine Dinucleotide | ||
DB03415 | acyl-CoA dehydrogenase, C-4 to C-12 straight chain | experimental | 3-Thiaoctanoyl-Coenzyme A |
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Cross referenced IDs for ACADM |
* 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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