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 APOC3
Basic gene info.Gene symbolAPOC3
Gene nameapolipoprotein C-III
SynonymsAPOCIII|HALP2
CytomapUCSC genome browser: 11q23.3
Genomic locationchr11 :116700623-116703787
Type of geneprotein-coding
RefGenesNM_000040.1,
Ensembl idENSG00000110245
Descriptionapo-CIIIapoC-IIIapolipoprotein C3
Modification date20141207
dbXrefs MIM : 107720
HGNC : HGNC
Ensembl : ENSG00000110245
HPRD : 00132
Vega : OTTHUMG00000046115
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APOC3
BioGPS: 345
Gene Expression Atlas: ENSG00000110245
The Human Protein Atlas: ENSG00000110245
PathwayNCI Pathway Interaction Database: APOC3
KEGG: APOC3
REACTOME: APOC3
ConsensusPathDB
Pathway Commons: APOC3
MetabolismMetaCyc: APOC3
HUMANCyc: APOC3
RegulationEnsembl's Regulation: ENSG00000110245
miRBase: chr11 :116,700,623-116,703,787
TargetScan: NM_000040
cisRED: ENSG00000110245
ContextiHOP: APOC3
cancer metabolism search in PubMed: APOC3
UCL Cancer Institute: APOC3
Assigned class in ccmGDBC

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Phenotypic Information for APOC3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: APOC3
Familial Cancer Database: APOC3
* 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: APOC3
MedGen: APOC3 (Human Medical Genetics with Condition)
ClinVar: APOC3
PhenotypeMGI: APOC3 (International Mouse Phenotyping Consortium)
PhenomicDB: APOC3

Mutations for APOC3
* 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 APOC3 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
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=9)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr11:116701581-116701581p.V50L2
chr11:116701535-116701535p.G34G1
chr11:116701559-116701559p.T42T1
chr11:116701560-116701560p.A43T1
chr11:116701579-116701579p.S49N1
chr11:116701317-116701317p.L7V1
chr11:116701610-116701610p.A59A1
chr11:116701336-116701336p.A13V1
chr11:116703480-116703480p.R60R1
chr11:116701354-116701354p.?1

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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
# sample1       1  23   21 1
# mutation1       1  23   21 1
nonsynonymous SNV           22      1
synonymous SNV1       1   1   21  
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
chr11:116701581p.V50L2
chr11:116701610p.S82S1
chr11:116703480p.P93Q1
chr11:116703546p.L7V1
chr11:116703578p.E22E1
chr11:116701317p.A23A1
chr11:116701499p.G34C1
chr11:116701502p.T42T1
chr11:116701533p.A59A1
chr11:116701559p.R60R1

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 APOC3 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 APOC3

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,APOC3,ARG1,C8A,C9,
CREB3L3,CRP,F2,FABP1,FGF23,HP,ITIH1,
MT1B,PLG,SERPINA7,SERPINC1,SLC17A2,SULT2A1,TM4SF5
ACSM2A,ACSM2B,AMN,APOC3,APOL4,BMP3,TBATA,
CHGA,CHGB,CPO,DBH,NDRG4,ORM1,ORM2,
PDZD7,PHOX2B,SLC18A1,SNORA14A,ST8SIA3,TH,TTC36

ALB,APOA1,APOA5,APOC3,C1orf185,RIIAD1,CEACAM16,
CFHR2,CFHR5,DRD1,F9,FGG,ITIH1,LGSN,
NEK10,NPHS2,RGS22,SERPINC1,SH3GL2,SPP2,ZDHHC11
AADAC,APOA1,APOA4,APOB,APOC3,C17orf78,CRISP1,
FAM99A,FAM99B,GSTA5,KCNJ13,LCE3E,LOC388428,MOS,
ONECUT3,OR10H1,OR10H5,OR4N5,PWAR4___F2RL3___PAWR,SLC2A2,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 APOC3
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
DB00363apolipoprotein C-IIIapprovedClozapine
DB00334apolipoprotein C-IIIapproved; investigationalOlanzapine
DB00503apolipoprotein C-IIIapproved; investigationalRitonavir


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Cross referenced IDs for APOC3
* 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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