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 CPT2
Basic gene info.Gene symbolCPT2
Gene namecarnitine palmitoyltransferase 2
SynonymsCPT1|CPTASE|IIAE4
CytomapUCSC genome browser: 1p32
Genomic locationchr1 :53662100-53679869
Type of geneprotein-coding
RefGenesNM_000098.2,
Ensembl idENSG00000157184
DescriptionCPT IIcarnitine O-palmitoyltransferase 2, mitochondrialcarnitine palmitoyltransferase II
Modification date20141219
dbXrefs MIM : 600650
HGNC : HGNC
Ensembl : ENSG00000157184
HPRD : 02802
Vega : OTTHUMG00000008942
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CPT2
BioGPS: 1376
Gene Expression Atlas: ENSG00000157184
The Human Protein Atlas: ENSG00000157184
PathwayNCI Pathway Interaction Database: CPT2
KEGG: CPT2
REACTOME: CPT2
ConsensusPathDB
Pathway Commons: CPT2
MetabolismMetaCyc: CPT2
HUMANCyc: CPT2
RegulationEnsembl's Regulation: ENSG00000157184
miRBase: chr1 :53,662,100-53,679,869
TargetScan: NM_000098
cisRED: ENSG00000157184
ContextiHOP: CPT2
cancer metabolism search in PubMed: CPT2
UCL Cancer Institute: CPT2
Assigned class in ccmGDBC

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Phenotypic Information for CPT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CPT2
Familial Cancer Database: CPT2
* 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: CPT2
MedGen: CPT2 (Human Medical Genetics with Condition)
ClinVar: CPT2
PhenotypeMGI: CPT2 (International Mouse Phenotyping Consortium)
PhenomicDB: CPT2

Mutations for CPT2
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CPT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA531596CPT2368615367919753679247CPT26838815367919753679869

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
There's no copy number variation information in COSMIC data for this gene.

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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=38)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr1:53676857-53676857p.P504L3
chr1:53676448-53676448p.V368I2
chr1:53679229-53679229p.M647V2
chr1:53676386-53676386p.G347D2
chr1:53675956-53675956p.A204T2
chr1:53675969-53675969p.N208S1
chr1:53679099-53679099p.A603A1
chr1:53676407-53676407p.K354T1
chr1:53676697-53676697p.G451*1
chr1:53675972-53675972p.A209V1

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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
# sample 5 51 11   422  24 7
# mutation 5 41 11   422  25 7
nonsynonymous SNV 5 31 11   322   5 4
synonymous SNV   1       1    2  3
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
chr1:53676799p.T485P2
chr1:53676038p.P284P1
chr1:53676551p.N585S1
chr1:53679049p.H337Q1
chr1:53676067p.L587L1
chr1:53676593p.K354T1
chr1:53679099p.A603A1
chr1:53676140p.P53L1
chr1:53676597p.G375S1
chr1:53666396p.G609G1

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 CPT2 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 CPT2

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,ALDH6A1,ATPAF1,BSDC1,C1orf210,TCEANC2,CPT2,
DHCR24,IPP,IVD,KIAA0319L,MYCBP,NRD1,NSUN4,
OMA1,PAFAH2,PARS2,POMGNT1,SCP2,TMEM59,YIPF1
ABCB6,ACADM,AIFM1,MPC2,C19orf54,GUCD1,COQ6,
CPT2,CRAT,CSPG5,DBI,GRPEL1,HIST1H1C,IVD,
LDHD,NDUFA10,NDUFAF1,NFS1,PCCB,ECI2,SUOX

ABCD3,ACADS,ALDH6A1,ARHGEF16,C1orf210,CPT2,DLST,
ETFDH,GGT6,GPBP1L1,HMGCL,LDHD,NUDT6,OMA1,
PAFAH2,PIGR,RBM47,RPS6KA1,SCP2,SIAE,TMEM125
ACSF2,AGFG2,AP1M2,BDH1,CPT2,DTX4,ENTPD5,
EPB41L4B,KLF5,LDLRAP1,MARVELD3,MYO1D,PAFAH2,PLD1,
PPARG,PTK6,SFXN5,SH3BGRL2,SLC44A1,TRAF3IP2,WDR78
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 CPT2
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 2approvedL-Carnitine
DB01074carnitine palmitoyltransferase 2approvedPerhexiline
DB01076carnitine palmitoyltransferase 2approvedAtorvastatin
DB00439carnitine palmitoyltransferase 2withdrawnCerivastatin
DB01095carnitine palmitoyltransferase 2approvedFluvastatin
DB00175carnitine palmitoyltransferase 2approvedPravastatin
DB01098carnitine palmitoyltransferase 2approvedRosuvastatin
DB00641carnitine palmitoyltransferase 2approvedSimvastatin


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Cross referenced IDs for CPT2
* 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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