Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	APOA2
	Gene name	apolipoprotein A-II
	Synonyms	Apo-AII\|ApoA-II\|apoAII
	Cytomap	UCSC genome browser: 1q23.3
	Genomic location	chr1 :161192082-161193418
	Type of gene	protein-coding
	RefGenes	NM_001643.1,
	Ensembl id	ENSG00000158874
	Description	apolipoprotein A2
	Modification date	20141207
dbXrefs	MIM : 107670
	HGNC : HGNC
	Ensembl : ENSG00000158874
	HPRD : 00129
	Vega : OTTHUMG00000034346
Protein	UniProt: P02652 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_APOA2
	BioGPS: 336
	Gene Expression Atlas: ENSG00000158874
	The Human Protein Atlas: ENSG00000158874
Pathway	NCI Pathway Interaction Database: APOA2
	KEGG: APOA2
	REACTOME: APOA2
	ConsensusPathDB
	Pathway Commons: APOA2
Metabolism	MetaCyc: APOA2
	HUMANCyc: APOA2
Regulation	Ensembl's Regulation: ENSG00000158874
	miRBase: chr1 :161,192,082-161,193,418
	TargetScan: NM_001643
	cisRED: ENSG00000158874
Context	iHOP: APOA2
	cancer metabolism search in PubMed: APOA2
	UCL Cancer Institute: APOA2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

Top

Phenotypic Information for APOA2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_LIPOPROTEIN_METABOLISM

Others
OMIM	107670; gene+phenotype.
Orphanet	238269; Familial renal amyloidosis due to Apolipoprotein AII variant.
Disease	KEGG Disease: APOA2
	MedGen: APOA2 (Human Medical Genetics with Condition)
	ClinVar: APOA2
Phenotype	MGI: APOA2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows APOA2 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BG562889	SAA1	1	266	11	18287811	18290879	APOA2	266	518	1	161192152	161192799
AI064980	DEFA1	1	480	8	6854300	6856718	APOA2	469	601	1	161192236	161192764
AF063569	APOA2	20	274	1	161192082	161192731	PFKFB2	267	604	1	207221981	207222316
AI110694	APOA2	20	274	1	161192082	161192731	PFKFB2	267	604	1	207221981	207222316
AI207725	APOA2	1	470	1	161192082	161193414	SND1	466	601	7	127732510	127732645
AI336287	FHL3	9	410	1	38462445	38462846	APOA2	407	460	1	161192762	161192815
AI064779	APOA2	21	494	1	161192082	161193418	PNP	492	553	14	20944930	20944991
AF090896	APOA2	20	274	1	161192082	161192731	PFKFB2	267	2907	1	207219676	207222316

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

Top

SNV 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

Top

Somatic 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.

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr1:161192228-161192228	p.F90F	3
chr1:161193180-161193180	p.L4L	1
chr1:161192260-161192260	p.G80*	1
chr1:161193191-161193191	p.M1V	1
chr1:161192276-161192276	p.P74P	1
chr1:161192291-161192291	p.K69N	1
chr1:161192316-161192316	p.?	1
chr1:161192745-161192745	p.E50K	1
chr1:161192794-161192794	p.L33L	1
chr1:161192819-161192819	p.A25E	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1			1			1					2					2	2		3
# mutation	1			1			1					3					2	2		3
nonsynonymous SNV	1			1			1											1		2
synonymous SNV												3					2	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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr1:161192228	p.F90F	3
chr1:161192255	p.T81T	1
chr1:161192291	p.K69N	1
chr1:161192312	p.K62K	1
chr1:161192794	p.L33L	1
chr1:161193167	p.L9I	1
chr1:161193180	p.L4L	1
chr1:161193191	p.M1V	1
chr1:161192205	p.A98D	1
chr1:161192214	p.T95K	1

Other 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

Copy 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]

Top

Gene Expression for APOA2

Gene 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.

Differential 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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

Gene-Gene Network Information

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for APOA2

There's no related Drug.

Top

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