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 CPT1A
Basic gene info.Gene symbolCPT1A
Gene namecarnitine palmitoyltransferase 1A (liver)
SynonymsCPT1|CPT1-L|L-CPT1
CytomapUCSC genome browser: 11q13.2
Genomic locationchr11 :68522087-68609399
Type of geneprotein-coding
RefGenesNM_001031847.2,
NM_001876.3,
Ensembl idENSG00000110090
DescriptionCPT ICPTI-Lcarnitine O-palmitoyltransferase 1, liver isoformcarnitine O-palmitoyltransferase I, liver isoformcarnitine palmitoyltransferase I, liver
Modification date20141219
dbXrefs MIM : 600528
HGNC : HGNC
Ensembl : ENSG00000110090
HPRD : 02755
Vega : OTTHUMG00000167892
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CPT1A
BioGPS: 1374
Gene Expression Atlas: ENSG00000110090
The Human Protein Atlas: ENSG00000110090
PathwayNCI Pathway Interaction Database: CPT1A
KEGG: CPT1A
REACTOME: CPT1A
ConsensusPathDB
Pathway Commons: CPT1A
MetabolismMetaCyc: CPT1A
HUMANCyc: CPT1A
RegulationEnsembl's Regulation: ENSG00000110090
miRBase: chr11 :68,522,087-68,609,399
TargetScan: NM_001031847
cisRED: ENSG00000110090
ContextiHOP: CPT1A
cancer metabolism search in PubMed: CPT1A
UCL Cancer Institute: CPT1A
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CPT1A in cancer cell metabolism1. Patsoukis N, Bardhan K, Chatterjee P, Sari D, Liu B, et al. (2015) PD-1 alters T-cell metabolic reprogramming by inhibiting glycolysis and promoting lipolysis and fatty acid oxidation. Nat Commun 6: 6692. doi: 10.1038/ncomms7692. pmid: 4389235. go to article
2. Patella F, Schug ZT, Persi E, Neilson LJ, Erami Z, et al. (2015) Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability. Mol Cell Proteomics 14: 621-634. doi: 10.1074/mcp.M114.045575. pmid: 4349982. go to article
3. Roy D, Mondal S, Wang C, He X, Khurana A, et al. (2014) Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer. Cancer Metab 2: 13. doi: 10.1186/2049-3002-2-13. pmid: 4164348. go to article
4. Schlaepfer IR, Rider L, Rodrigues LU, Gijon MA, Pac CT, et al. (2014) Lipid catabolism via CPT1 as a therapeutic target for prostate cancer. Mol Cancer Ther 13: 2361-2371. doi: 10.1158/1535-7163.MCT-14-0183. pmid: 4185227. go to article
5. Cirillo A, Di Salle A, Petillo O, Melone MA, Grimaldi G, et al. (2014) High grade glioblastoma is associated with aberrant expression of ZFP57, a protein involved in gene imprinting, and of CPT1A and CPT1C that regulate fatty acid metabolism. Cancer Biol Ther 15: 735-741. doi: 10.4161/cbt.28408. pmid: 4049789. go to article

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Phenotypic Information for CPT1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CPT1A
Familial Cancer Database: CPT1A
* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CPT1A
MedGen: CPT1A (Human Medical Genetics with Condition)
ClinVar: CPT1A
PhenotypeMGI: CPT1A (International Mouse Phenotyping Consortium)
PhenomicDB: CPT1A

Mutations for CPT1A
* 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
haematopoietic_and_lymphoid_tissueCPT1Achr116856788668567886CPT1Achr116856788668567886
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 CPT1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK309464CPT1A11887116854073268607152RDH518852165125611766856118220
BM970771CPT1A15152116852235168522488C16orf721476341692102679210755
BM041208CPT1A2681116855243168575053GAPDH6627051266474946647537
CB154699CPT1A15243116852318168523409FGG2325374155525288155526135

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 # sample23     1 5     1 1
GAIN (# sample)23     1 4     1 1
LOSS (# sample)        1        
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=61)
Stat. for Synonymous SNVs
(# total SNVs=23)
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
chr11:68566686-68566686p.Y231Y3
chr11:68582853-68582853p.Q30H2
chr11:68540835-68540835p.F546F2
chr11:68552320-68552320p.G376R2
chr11:68579905-68579905p.A94V2
chr11:68549256-68549256p.H445H2
chr11:68571514-68571514p.S170L2
chr11:68552398-68552398p.D350N2
chr11:68548126-68548126p.I480I2
chr11:68542876-68542876p.Q495*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
# sample34 182 10    1073  158 10
# mutation34 182 10    1173  158 13
nonsynonymous SNV23 141 4    1042  97 9
synonymous SNV11 41 6    131  61 4
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
chr11:68571514p.S170L,CPT1A3
chr11:68549256p.Q30H,CPT1A2
chr11:68582853p.H445H,CPT1A2
chr11:68548126p.I480I,CPT1A2
chr11:68579905p.A94V,CPT1A2
chr11:68542866p.R563H,CPT1A1
chr11:68566686p.L469I,CPT1A1
chr11:68525121p.P302S,CPT1A1
chr11:68529012p.V179V,CPT1A1
chr11:68549243p.D698H,CPT1A1

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 CPT1A 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 CPT1A

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

BRCA1,CCND1,CHD6,CPT1A,CTTN,DNAJC14,FADD,
FITM2,IGHMBP2,KIF3B,MRPL21,MTL5,ORAOV1,PANK3,
PPFIA1,PPP6R3,SCD,SUV420H1,TMED10P1,VPS13B,ZNF623
ABL2,ADD2,ANGPT2,ARHGAP23,ATP8B2,BMX,CMIP,
CPT1A,DOC2B,ELF4,KCNT2,LHX6,NOD1,PLSCR1,
RPGR,SEPT8,SWAP70,TLL1,TMOD2,TRPM6,ZNF385D

AIFM3,AMBRA1,CPT1A,CTTN,DAGLA,FABP1,TMEM236,
FZD5,GPD1L,HMGCS2,KALRN,KCNK5,LOC25845,MYB,
OVOL1,PITPNM1,PPFIA1,SGK2,SLC35D3,SLC9A3,UBE4A
ABCC3,ACOX1,AGFG2,CD2AP,CDH1,CPT1A,CUL3,
EPB41L4B,FLNB,FZD5,HNF4A,PDCD6IP,PDE8A,RAPGEFL1,
RBM47,SGK2,SLC41A2,STK38,TMEM63B,TNK1,TRAPPC10
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 CPT1A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00583carnitine palmitoyltransferase 1A (liver)approvedL-Carnitine
DB01074carnitine palmitoyltransferase 1A (liver)approvedPerhexiline


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Cross referenced IDs for CPT1A
* 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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