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 APOA2
Basic gene info.Gene symbolAPOA2
Gene nameapolipoprotein A-II
SynonymsApo-AII|ApoA-II|apoAII
CytomapUCSC genome browser: 1q23.3
Genomic locationchr1 :161192082-161193418
Type of geneprotein-coding
RefGenesNM_001643.1,
Ensembl idENSG00000158874
Descriptionapolipoprotein A2
Modification date20141207
dbXrefs MIM : 107670
HGNC : HGNC
Ensembl : ENSG00000158874
HPRD : 00129
Vega : OTTHUMG00000034346
ProteinUniProt: P02652
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APOA2
BioGPS: 336
Gene Expression Atlas: ENSG00000158874
The Human Protein Atlas: ENSG00000158874
PathwayNCI Pathway Interaction Database: APOA2
KEGG: APOA2
REACTOME: APOA2
ConsensusPathDB
Pathway Commons: APOA2
MetabolismMetaCyc: APOA2
HUMANCyc: APOA2
RegulationEnsembl's Regulation: ENSG00000158874
miRBase: chr1 :161,192,082-161,193,418
TargetScan: NM_001643
cisRED: ENSG00000158874
ContextiHOP: APOA2
cancer metabolism search in PubMed: APOA2
UCL Cancer Institute: APOA2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for APOA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: APOA2
Familial Cancer Database: APOA2
* 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 107670; gene+phenotype.
Orphanet 238269; Familial renal amyloidosis due to Apolipoprotein AII variant.
DiseaseKEGG Disease: APOA2
MedGen: APOA2 (Human Medical Genetics with Condition)
ClinVar: APOA2
PhenotypeMGI: APOA2 (International Mouse Phenotyping Consortium)
PhenomicDB: APOA2

Mutations for APOA2
* 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 APOA2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG562889SAA11266111828781118290879APOA22665181161192152161192799
AI064980DEFA11480868543006856718APOA24696011161192236161192764
AF063569APOA2202741161192082161192731PFKFB22676041207221981207222316
AI110694APOA2202741161192082161192731PFKFB22676041207221981207222316
AI207725APOA214701161192082161193414SND14666017127732510127732645
AI336287FHL3941013846244538462846APOA24074601161192762161192815
AI064779APOA2214941161192082161193418PNP492553142094493020944991
AF090896APOA2202741161192082161192731PFKFB226729071207219676207222316

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=5)
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
chr1:161192228-161192228p.F90F3
chr1:161192316-161192316p.?1
chr1:161192745-161192745p.E50K1
chr1:161192794-161192794p.L33L1
chr1:161192819-161192819p.A25E1
chr1:161192205-161192205p.A98D1
chr1:161193162-161193162p.L10L1
chr1:161193167-161193167p.L9L1
chr1:161192240-161192240p.F86L1
chr1:161193179-161193179p.A5T1

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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
# sample1  1  1    2    22 3
# mutation1  1  1    3    22 3
nonsynonymous SNV1  1  1          1 2
synonymous SNV           3    21 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
chr1:161192228p.F90F3
chr1:161192794p.M1V1
chr1:161193167p.A98D1
chr1:161193180p.T95K1
chr1:161193191p.F86L1
chr1:161192205p.T81T1
chr1:161192214p.K69N1
chr1:161192240p.K62K1
chr1:161192255p.L33L1
chr1:161192291p.L9I1

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 APOA2 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 APOA2

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

APCS,APOA2,APOA4,APOB,APOC3,ARG1,C8A,
C9,CREB3L3,CRP,F2,FABP1,FGF23,HP,
ITIH1,MT1B,PLG,SERPINA7,SERPINC1,SLC17A2,TM4SF5
ACSM2B,APOA2,APOC3,APOL4,TBATA,CHGA,CYP3A5,
DBH,DEFA5,GRAPL,IFNL3,KCNG4,LOC100133469,NDRG4,
ORM2,PHOX2B,POU4F2,SLC18A1,SNORA14A,ST8SIA3,TH

AMBP,APOA2,ATP4A,C1orf64,CHRND,DCT,F2,
FAM71E2,GYPB,HHATL,HIST1H4G,IGDCC3,IGF2BP1,KLK2,
MLANA,LINC00202-1,OC90,OR6C68,PLSCR5,SNAR-F,TXNDC8
ALB,APCS,APOA2,C3P1,C8A,CFHR2,CFHR5,
CYP4A22,DNAJB8,F13B,F9,FGG,HRG,KIR3DP1,
KRTAP4-11,KRTAP5-3,LECT2,LOC100129935,LINC00160,OR1N1,SLC17A2
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 APOA2


There's no related Drug.
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Cross referenced IDs for APOA2
* 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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