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 CETP
Basic gene info.Gene symbolCETP
Gene namecholesteryl ester transfer protein, plasma
SynonymsBPIFF|HDLCQ10
CytomapUCSC genome browser: 16q21
Genomic locationchr16 :56995834-57017756
Type of geneprotein-coding
RefGenesNM_000078.2,
NM_001286085.1,
Ensembl idENSG00000087237
DescriptionBPI fold containing family Fcholesteryl ester transfer proteinlipid transfer protein I
Modification date20141222
dbXrefs MIM : 118470
HGNC : HGNC
Ensembl : ENSG00000087237
HPRD : 00325
Vega : OTTHUMG00000133279
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CETP
BioGPS: 1071
Gene Expression Atlas: ENSG00000087237
The Human Protein Atlas: ENSG00000087237
PathwayNCI Pathway Interaction Database: CETP
KEGG: CETP
REACTOME: CETP
ConsensusPathDB
Pathway Commons: CETP
MetabolismMetaCyc: CETP
HUMANCyc: CETP
RegulationEnsembl's Regulation: ENSG00000087237
miRBase: chr16 :56,995,834-57,017,756
TargetScan: NM_000078
cisRED: ENSG00000087237
ContextiHOP: CETP
cancer metabolism search in PubMed: CETP
UCL Cancer Institute: CETP
Assigned class in ccmGDBC

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

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

Mutations for CETP
* 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 CETP 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 # sample1             1  
GAIN (# sample)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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr16:57017553-57017553p.V486A3
chr16:57003556-57003556p.I134I3
chr16:57012109-57012109p.V363A3
chr16:56996995-56996995p.K64K2
chr16:57003319-57003319p.S85S2
chr16:57017290-57017290p.F458F2
chr16:56995952-56995952p.G21S2
chr16:57003551-57003551p.E133K1
chr16:57007404-57007404p.L304L1
chr16:57004986-57004986p.F190Y1

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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
# sample11 122 4    6    9416
# mutation11 112 4    6    14416
nonsynonymous SNV11 81 2    4    63 5
synonymous SNV   31 2    2    8111
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
chr16:57012109p.V303A,CETP3
chr16:57015105p.K334N,CETP2
chr16:57003556p.I134I,CETP2
chr16:57004978p.G21G,CETP1
chr16:57007305p.F184L,CETP1
chr16:57003370p.E263D,CETP1
chr16:57015098p.E422K,CETP1
chr16:57004989p.L37L,CETP1
chr16:57007351p.F187F,CETP1
chr16:57003380p.S274R,CETP1

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 CETP 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 CETP

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

ACVRL1,MILR1,C1orf54,CD209,CD248,CETP,CLEC4G,
CYGB,DNASE1L3,EMP3,FOLR2,GMFG,GRAP,NCF4,
POPDC2,PSTPIP1,PTGDS,SH2D3C,STAB1,TNFAIP8L2,WAS
CCL18,CEACAM3,CETP,CTSL,FBN1,GAD2,GAP43,
HMOX1,LGI2,OR2AG1,OR8D1,RHOXF2B,SLC48A1,SNORA19,
SPATA8,SPRR2F,TECTB,TMEM150B,VENTXP1,WNT10B,WNT1

ADCY4,AFAP1L1,ALPK2,ARHGEF15,CCDC102B,CD34,CETP,
CHST1,CLEC1A,CUBN,CXorf36,ELTD1,FBLN7,FLI1,
GIPC3,GPR116,NOTCH4,PCDH12,SH2D3C,STK32B,USHBP1
ARHGAP25,BTN2A2,C1orf228,CETP,CMTM7,CR1,FUT7,
FXYD5,GPSM3,GRHL3,HLA-DOA,HVCN1,KCNAB2,LOC283999,
LTF,NKX6-3,OPRL1,SERPINB7,TCN1,ZBED2,ZBTB32
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 CETP
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
DB01095cholesteryl ester transfer protein, plasmaapprovedFluvastatin
DB01076cholesteryl ester transfer protein, plasmaapprovedAtorvastatin
DB00175cholesteryl ester transfer protein, plasmaapprovedPravastatin
DB00264cholesteryl ester transfer protein, plasmaapproved; investigationalMetoprolol


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Cross referenced IDs for CETP
* 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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