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 ACADM
Basic gene info.Gene symbolACADM
Gene nameacyl-CoA dehydrogenase, C-4 to C-12 straight chain
SynonymsACAD1|MCAD|MCADH
CytomapUCSC genome browser: 1p31
Genomic locationchr1 :76190042-76229355
Type of geneprotein-coding
RefGenesNM_000016.5,
NM_001127328.2,NM_001286042.1,NM_001286043.1,NM_001286044.1,
NR_022013.1,
Ensembl idENSG00000117054
Descriptionacyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chainmedium-chain specific acyl-CoA dehydrogenase, mitochondrial
Modification date20141222
dbXrefs MIM : 607008
HGNC : HGNC
Ensembl : ENSG00000117054
HPRD : 08447
Vega : OTTHUMG00000009784
ProteinUniProt: P11310
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACADM
BioGPS: 34
Gene Expression Atlas: ENSG00000117054
The Human Protein Atlas: ENSG00000117054
PathwayNCI Pathway Interaction Database: ACADM
KEGG: ACADM
REACTOME: ACADM
ConsensusPathDB
Pathway Commons: ACADM
MetabolismMetaCyc: ACADM
HUMANCyc: ACADM
RegulationEnsembl's Regulation: ENSG00000117054
miRBase: chr1 :76,190,042-76,229,355
TargetScan: NM_000016
cisRED: ENSG00000117054
ContextiHOP: ACADM
cancer metabolism search in PubMed: ACADM
UCL Cancer Institute: ACADM
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ACADM in cancer cell metabolism1. 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)
check002.gifCancer Description
Cancer CGAP: ACADM
Familial Cancer Database: ACADM
* 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_FATTY_ACID_METABOLISM
KEGG_BETA_ALANINE_METABOLISM
KEGG_PROPANOATE_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 201450; phenotype.
607008; gene.
Orphanet 42; Medium chain acyl-CoA dehydrogenase deficiency.
DiseaseKEGG Disease: ACADM
MedGen: ACADM (Human Medical Genetics with Condition)
ClinVar: ACADM
PhenotypeMGI: 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.

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
ovaryACADMchr17620368276203702ACADMchr17620801276208032
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 ACADM 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 # 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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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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr1:76215151-76215151p.F252F3
chr1:76199306-76199306p.S127F3
chr1:76205779-76205779p.G195R3
chr1:76205781-76205781p.G195G3
chr1:76198353-76198353p.F48C2
chr1:76199293-76199293p.I123V2
chr1:76200483-76200483p.P132L2
chr1:76200514-76200514p.K142N1
chr1:76194107-76194107p.F18L1
chr1:76211520-76211520p.D210V1

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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
# sample   11  3 1  513  73 10
# mutation   8  3 1  513  73 10
nonsynonymous SNV   5  3 1  512  63 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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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
chr1:76205781p.G6G,ACADM3
chr1:76215151p.F63F,ACADM3
chr1:76199306p.S91Y,ACADM2
chr1:76198353p.F12C,ACADM2
chr1:76205779p.A205V,ACADM1
chr1:76194134p.R17C,ACADM1
chr1:76216213p.I3M,ACADM1
chr1:76199254p.L220R,ACADM1
chr1:76194141p.P26R,ACADM1
chr1:76226820p.G6R,ACADM1

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 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

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

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
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 ACADM
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA24425; -.
Organism-specific databasesCTD 34; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02910acyl-CoA dehydrogenase, C-4 to C-12 straight chainexperimentalOctanoyl-Coenzyme A
DB03147acyl-CoA dehydrogenase, C-4 to C-12 straight chainexperimentalFlavin-Adenine Dinucleotide
DB03415acyl-CoA dehydrogenase, C-4 to C-12 straight chainexperimental3-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

: Open all cross reference information



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