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

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 ABCG8

Basic gene info.	Gene symbol	ABCG8
	Gene name	ATP-binding cassette, sub-family G (WHITE), member 8
	Synonyms	GBD4\|STSL
	Cytomap	UCSC genome browser: 2p21
	Genomic location	chr2 :44066102-44105605
	Type of gene	protein-coding
	RefGenes	NM_022437.2,
	Ensembl id	ENSG00000143921
	Description	ATP-binding cassette sub-family G member 8ATP-binding cassette, subfamily G, member 8sterolin 2sterolin-2
	Modification date	20141222
dbXrefs	MIM : 605460
	HGNC : HGNC
	Ensembl : ENSG00000143921
	HPRD : 05679
	Vega : OTTHUMG00000128756
Protein	UniProt: Q9H221 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ABCG8
	BioGPS: 64241
	Gene Expression Atlas: ENSG00000143921
	The Human Protein Atlas: ENSG00000143921
Pathway	NCI Pathway Interaction Database: ABCG8
	KEGG: ABCG8
	REACTOME: ABCG8
	ConsensusPathDB
	Pathway Commons: ABCG8
Metabolism	MetaCyc: ABCG8
	HUMANCyc: ABCG8
Regulation	Ensembl's Regulation: ENSG00000143921
	miRBase: chr2 :44,066,102-44,105,605
	TargetScan: NM_022437
	cisRED: ENSG00000143921
Context	iHOP: ABCG8
	cancer metabolism search in PubMed: ABCG8
	UCL Cancer Institute: ABCG8
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ABCG8 in cancer cell metabolism	1. Hlavata I, Mohelnikova-Duchonova B, Vaclavikova R, Liska V, Pitule P, et al. (2012) The role of ABC transporters in progression and clinical outcome of colorectal cancer. Mutagenesis 27: 187-196. doi: 10.1093/mutage/ger075. go to article 2. Patel SB (2014) Recent advances in understanding the STSL locus and ABCG5/ABCG8 biology. Curr Opin Lipidol 25: 169-175. doi: 10.1097/MOL.0000000000000071. go to article

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Phenotypic Information for ABCG8(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ABCG8
	Familial Cancer Database: ABCG8

* 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

Others
OMIM	210250; phenotype. 605460; gene. 611465; phenotype.
Orphanet	2882; Sitosterolemia.
Disease	KEGG Disease: ABCG8
	MedGen: ABCG8 (Human Medical Genetics with Condition)
	ClinVar: ABCG8
Phenotype	MGI: ABCG8 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ABCG8

Mutations for ABCG8

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ABCG8	chr2	44075465	44075485	ABCG8	chr2	44077242	44077262
pancreas	ABCG8	chr2	44079992	44080192	ZNF521	chr18	22892429	22892629

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ABCG8 related fusion information.

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

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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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

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=75)	Stat. for Synonymous SNVs (# total SNVs=27)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr2:44104775-44104775	p.R611I	3
chr2:44102409-44102409	p.V538G	3
chr2:44078951-44078951	p.R184H	3
chr2:44079912-44079912	p.T290I	2
chr2:44078853-44078853	p.V151V	2
chr2:44079531-44079531	p.C200C	2
chr2:44078854-44078854	p.R152C	2
chr2:44079618-44079618	p.W229*	2
chr2:44099383-44099383	p.T383T	2
chr2:44104812-44104812	p.A623A	2

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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	2	1	2	8	1		7		4		1	15	9	3			16	9	3	10
# mutation	2	1	2	11	1		8		4		1	15	10	3			21	9	3	12
nonsynonymous SNV			1	9	1		6		3		1	10	9	1			12	6	2	6
synonymous SNV	2	1	1	2			2		1			5	1	2			9	3	1	6

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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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
chr2:44078951	p.R184H	3
chr2:44079964	p.I307I	3
chr2:44079912	p.R597W	2
chr2:44101062	p.R611K	2
chr2:44104732	p.A450T	2
chr2:44104775	p.T290N	2
chr2:44079738	p.G232E	2
chr2:44102330	p.G574G	1
chr2:44078767	p.F71L	1
chr2:44099211	p.S140S	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 ABCG8 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 ABCG8

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))

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CNV 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

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


A1BG,ABCG5,ABCG8,ALG1L,LINC00313,LSMEM2,CA5A, F12,H3F3C,HAMP,HCCAT5,HYAL1,LEAP2,LOC84989, MT1A,MT1DP,MT1F,POMC,PTH2,RIMBP3C,TMEM82	ABCG8,ADH1B,TRABD2A,HILPDA,CIDEA,DEFA6,DSG4, ENOX1,GYS2,HADH,LOC283392,LOC401052,MAP3K5,NAALAD2, NIPSNAP3B,PDK4,RGS17,RNF125,SLC19A3,TM7SF2,UTS2B

ABCG5,ABCG8,ACBD5,CREG2,CTAGE5,FAM169B,FGD4, LYZ,MIA2,MLPH,MTMR10,MTUS1,PRSS12,PSAPL1, RAB27B,SEMA4B,SLC9A4,SOCS6,SSTR1,TRAK1,ZMYND12	AADAC,ABCG5,ABCG8,ALDOB,APOA1,APOA4,C17orf78, ERICH4,CEACAM20,CRISP1,DPEP1,ENPEP,FABP6,GSTA2, GSTA5,KCNJ13,ONECUT3,SLC2A2,SLC7A9,SPA

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

: Open all plots for all cancer types

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Interacting 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 ABCG8

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA24412; -.
Organism-specific databases	CTD	64241; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00973	ATP-binding cassette, sub-family G (WHITE), member 8	approved	Ezetimibe
DB01076	ATP-binding cassette, sub-family G (WHITE), member 8	approved	Atorvastatin
DB01095	ATP-binding cassette, sub-family G (WHITE), member 8	approved	Fluvastatin
DB00227	ATP-binding cassette, sub-family G (WHITE), member 8	approved; investigational	Lovastatin
DB00175	ATP-binding cassette, sub-family G (WHITE), member 8	approved	Pravastatin
DB01098	ATP-binding cassette, sub-family G (WHITE), member 8	approved	Rosuvastatin
DB00641	ATP-binding cassette, sub-family G (WHITE), member 8	approved	Simvastatin

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Cross referenced IDs for ABCG8

* 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