Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 APOE
Basic gene info.Gene symbolAPOE
Gene nameapolipoprotein E
SynonymsAD2|APO-E|LDLCQ5|LPG
CytomapUCSC genome browser: 19q13.2
Genomic locationchr19 :45409038-45412650
Type of geneprotein-coding
RefGenesNM_000041.3,
NM_001302688.1,NM_001302689.1,NM_001302690.1,NM_001302691.1,
Ensembl idENSG00000130203
Descriptionapolipoprotein E3
Modification date20141222
dbXrefs MIM : 107741
HGNC : HGNC
Ensembl : ENSG00000130203
HPRD : 00135
Vega : OTTHUMG00000128901
ProteinUniProt: P02649
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APOE
BioGPS: 348
Gene Expression Atlas: ENSG00000130203
The Human Protein Atlas: ENSG00000130203
PathwayNCI Pathway Interaction Database: APOE
KEGG: APOE
REACTOME: APOE
ConsensusPathDB
Pathway Commons: APOE
MetabolismMetaCyc: APOE
HUMANCyc: APOE
RegulationEnsembl's Regulation: ENSG00000130203
miRBase: chr19 :45,409,038-45,412,650
TargetScan: NM_000041
cisRED: ENSG00000130203
ContextiHOP: APOE
cancer metabolism search in PubMed: APOE
UCL Cancer Institute: APOE
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for APOE(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: APOE
Familial Cancer Database: APOE
* 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 104310; phenotype.
107741; gene+phenotype.
143890; phenotype.
269600; phenotype.
611771; phenotype.
Orphanet 158029; Sea-blue histiocytosis.
1648; Dementia with Lewy body.
238616; Alzheimer disease.
329481; Lipoprotein glomerulopathy.
406; Heterozygous familial hypercholesterolemia.
412; Hyperlipoproteinemia type 3.
DiseaseKEGG Disease: APOE
MedGen: APOE (Human Medical Genetics with Condition)
ClinVar: APOE
PhenotypeMGI: APOE (International Mouse Phenotyping Consortium)
PhenomicDB: APOE

Mutations for APOE
* 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 APOE related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI680935APOE175194541187545411949APOE65254194541105345411823
BF887510PNPLA7111089140375682140375781APOE105295194541108745411857
AK130027APOE1263194540905545411169HMGA1260177963421050434214007
AI147021APOE1376194541155645411931LUC7L3371451174880795248808031

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
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
chr19:45411139-45411139p.R56C2
chr19:45412306-45412306p.K251N2
chr19:45411993-45411993p.S147N1
chr19:45411097-45411097p.Q42*1
chr19:45411997-45411997p.T148T1
chr19:45411101-45411101p.R43L1
chr19:45412103-45412103p.A184T1
chr19:45411112-45411112p.A47T1
chr19:45412123-45412123p.R190R1
chr19:45411204-45411204p.E77E1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   1       2  1  3 1
# mutation   1       2  1  3 1
nonsynonymous SNV   1       1     1 1
synonymous SNV           1  1  2  
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
chr19:45411904p.A124A1
chr19:45411925p.K260K1
chr19:45412333p.R278L1
chr19:45412386p.A295A1
chr19:45412438p.E299E1
chr19:45412450p.R43L1
chr19:45411101p.A47T1
chr19:45411112p.R56C1
chr19:45411139p.R108W1
chr19:45411875p.A117A1

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 APOE 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 APOE

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

AIF1,APOE,MILR1,C1QA,CRYBB1,CYBA,DOK2,
EMP3,FERMT3,FOLR2,FTL,GPX1,GRN,LST1,
NCF4,OSCAR,PSTPIP1,PTGDS,SPI1,IGFLR1,TYROBP
ACSM2A,ACSM2B,APOE,ATF5,BSG,IZUMO4,EIF4EBP1,
ELFN1,FPGS,GCDH,GCHFR,LIME1,MEF2B,MPST,
NDRG4,PCYT2,PDZD7,PMM1,PQLC1,SNX8,TSPO

ACP5,APOC1,APOE,C1QA,C1QB,C1QC,CD300LF,
DNAJC5B,GPNMB,HAVCR2,HTRA4,IL4I1,ITGB2,LAIR1,
LILRB4,PRAM1,PTCRA,RAB42,SPI1,TREM2,TYROBP
APOC1,APOE,B4GALT3,CCDC22,CD300LF,DALRD3,EIF3D,
EIF3F,EMID1,GNB2L1,ICAM4,INTS5,OTOA,QTRT1,
RAB42,RPL13,RPL23A,RPLP2,RPS2,TNFRSF18,TNFRSF4
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 APOE
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA55; -.
Organism-specific databasesCTD 348; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01095apolipoprotein EapprovedFluvastatin
DB00459apolipoprotein EapprovedAcitretin
DB00175apolipoprotein EapprovedPravastatin
DB01241apolipoprotein EapprovedGemfibrozil
DB00989apolipoprotein Eapproved; investigationalRivastigmine
DB00412apolipoprotein Eapproved; investigationalRosiglitazone
DB01418apolipoprotein EapprovedAcenocoumarol
DB00982apolipoprotein EapprovedIsotretinoin
DB00682apolipoprotein EapprovedWarfarin
DB00843apolipoprotein EapprovedDonepezil
DB01039apolipoprotein EapprovedFenofibrate
DB00503apolipoprotein Eapproved; investigationalRitonavir
DB00382apolipoprotein EapprovedTacrine
DB00122apolipoprotein Eapproved; nutraceuticalCholine
DB00641apolipoprotein EapprovedSimvastatin
DB00674apolipoprotein EapprovedGalantamine
DB00334apolipoprotein Eapproved; investigationalOlanzapine
DB00264apolipoprotein Eapproved; investigationalMetoprolol


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Cross referenced IDs for APOE
* 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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