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 APOA1
Basic gene info.Gene symbolAPOA1
Gene nameapolipoprotein A-I
Synonyms-
CytomapUCSC genome browser: 11q23-q24
Genomic locationchr11 :116706468-116708338
Type of geneprotein-coding
RefGenesNM_000039.1,
Ensembl idENSG00000118137
Descriptionapo-AI
Modification date20141222
dbXrefs MIM : 107680
HGNC : HGNC
Ensembl : ENSG00000118137
HPRD : 02517
Vega : OTTHUMG00000046112
ProteinUniProt: P02647
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APOA1
BioGPS: 335
Gene Expression Atlas: ENSG00000118137
The Human Protein Atlas: ENSG00000118137
PathwayNCI Pathway Interaction Database: APOA1
KEGG: APOA1
REACTOME: APOA1
ConsensusPathDB
Pathway Commons: APOA1
MetabolismMetaCyc: APOA1
HUMANCyc: APOA1
RegulationEnsembl's Regulation: ENSG00000118137
miRBase: chr11 :116,706,468-116,708,338
TargetScan: NM_000039
cisRED: ENSG00000118137
ContextiHOP: APOA1
cancer metabolism search in PubMed: APOA1
UCL Cancer Institute: APOA1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of APOA1 in cancer cell metabolism1. Guo X, Hao Y, Kamilijiang M, Hasimu A, Yuan J, et al. (2015) Potential predictive plasma biomarkers for cervical cancer by 2D-DIGE proteomics and Ingenuity Pathway Analysis. Tumour Biol 36: 1711-1720. doi: 10.1007/s13277-014-2772-5. go to article

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Phenotypic Information for APOA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: APOA1
Familial Cancer Database: APOA1
* 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 105200; phenotype.
107680; gene+phenotype.
205400; phenotype.
604091; phenotype.
Orphanet 314701; Primary systemic amyloidosis.
425; Apolipoprotein A-I deficiency.
93560; Familial renal amyloidosis due to Apolipoprotein AI variant.
DiseaseKEGG Disease: APOA1
MedGen: APOA1 (Human Medical Genetics with Condition)
ClinVar: APOA1
PhenotypeMGI: APOA1 (International Mouse Phenotyping Consortium)
PhenomicDB: APOA1

Mutations for APOA1
* 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 APOA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BJ995037APOA1135111116707015116708338DRAP1344438116568695865687288

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=17)
Stat. for Synonymous SNVs
(# total SNVs=1)
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
chr11:116707013-116707013p.G105G3
chr11:116707832-116707832p.Q29fs*72
chr11:116708063-116708063p.T14M2
chr11:116708076-116708076p.V10M2
chr11:116706998-116706998p.M110I1
chr11:116707771-116707771p.S49N1
chr11:116706556-116706556p.E258Q1
chr11:116707802-116707802p.A39T1
chr11:116706562-116706562p.A256S1
chr11:116707048-116707048p.E94K1

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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 1       3    36 2
# mutation 1 1       4    36 2
nonsynonymous SNV   1       3    26 2
synonymous SNV 1         1    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
chr11:116707117p.E258Q1
chr11:116706556p.G15V1
chr11:116707737p.A256T1
chr11:116706562p.A4V1
chr11:116707761p.E229E1
chr11:116706641p.R177S1
chr11:116707771p.R173H1
chr11:116706799p.E134A1
chr11:116707809p.E94K1
chr11:116706810p.Q93P1

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 APOA1 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 APOA1

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,APOA1,APOA2,APOA4,APOC3,C3P1,C8A,
C9,CREB3L3,CRP,F2,FABP1,FGF23,ITIH1,
MT1B,PLG,SERPINA7,SERPINC1,SLC17A2,SULT2A1,TM4SF5
AP2S1,APOA1,ARPC5L,LBHD1___C11orf98,MIEN1,CFL1,CHCHD1,
HM13,LENG9,MRPL17,MRPL27,MYEOV2,NR2F6,PPP1CA,
PPP4C,PSMC4,REEP4,SAMD1,TMEM8A,TXNL4A,YIF1B

AFM,ALB,APOA1,APOA4,APOB,APOC3,APOH,
CYP4F30P,CFHR2,CPO,FMO9P,GC,GP2,HRG,
ITIH1,KCNJ13,MS4A10,PCDHA13,PCDHA1,PIK3C2G,VTN
AADAC,APOA1,APOA4,APOB,APOC3,C17orf78,CPO,
CRISP1,FAM99A,FAM99B,GSTA5,KCNJ13,LCE3E,LOC388428,
MOS,ONECUT3,OR10H1,OR10H5,OR4N5,PWAR4___F2RL3___PAWR,SPANXN3
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 APOA1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL5984; -.
Organism-specific databasesPharmGKB PA49; -.
Organism-specific databasesCTD 335; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01039apolipoprotein A-IapprovedFenofibrate
DB00503apolipoprotein A-Iapproved; investigationalRitonavir
DB00624apolipoprotein A-Iapproved; investigationalTestosterone


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Cross referenced IDs for APOA1
* 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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