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 ABCC3

Basic gene info.	Gene symbol	ABCC3
	Gene name	ATP-binding cassette, sub-family C (CFTR/MRP), member 3
	Synonyms	ABC31\|EST90757\|MLP2\|MOAT-D\|MRP3\|cMOAT2
	Cytomap	UCSC genome browser: 17q22
	Genomic location	chr17 :48712217-48769063
	Type of gene	protein-coding
	RefGenes	NM_001144070.1, NM_003786.3,NM_020037.1,NM_020038.1,
	Ensembl id	ENSG00000108846
	Description	ATP-binding cassette sub-family C member 3canalicular multispecific organic anion transporter 2canicular multispecific organic anion transportermulti-specific organic anion transporter Dmultidrug resistance associated proteinmultidrug resistance-asso
	Modification date	20141207
dbXrefs	MIM : 604323
	HGNC : HGNC
	Ensembl : ENSG00000108846
	HPRD : 06826
	Vega : OTTHUMG00000162245
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ABCC3
	BioGPS: 8714
	Gene Expression Atlas: ENSG00000108846
	The Human Protein Atlas: ENSG00000108846
Pathway	NCI Pathway Interaction Database: ABCC3
	KEGG: ABCC3
	REACTOME: ABCC3
	ConsensusPathDB
	Pathway Commons: ABCC3
Metabolism	MetaCyc: ABCC3
	HUMANCyc: ABCC3
Regulation	Ensembl's Regulation: ENSG00000108846
	miRBase: chr17 :48,712,217-48,769,063
	TargetScan: NM_001144070
	cisRED: ENSG00000108846
Context	iHOP: ABCC3
	cancer metabolism search in PubMed: ABCC3
	UCL Cancer Institute: ABCC3
Assigned class in ccmGDB	C

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Phenotypic Information for ABCC3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ABCC3
	Familial Cancer Database: ABCC3

* 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
Orphanet
Disease	KEGG Disease: ABCC3
	MedGen: ABCC3 (Human Medical Genetics with Condition)
	ClinVar: ABCC3
Phenotype	MGI: ABCC3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ABCC3

Mutations for ABCC3

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	ABCC3	chr17	48760454	48760474		chr20	12935108	12935128

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 ABCC3 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
AW450940	ERCC6L2	13	211	9	98776644	98776842	ABCC3	207	390	17	48738088	48738271
AK000791	ABCC3	1	2578	17	48766883	48769460	ABCC3	2572	3327	17	48765523	48766278
BQ302632	ABCC3	20	377	17	48760952	48761501	DLGAP2	366	400	8	1456800	1506271
AI761355	YWHAZ	1	190	8	101951468	101951657	ABCC3	188	273	17	48721338	48721423
AI905457	ABCC3	20	182	17	48724032	48724193	ABCC3	177	609	17	48724397	48724829
AI905516	ABCC3	20	182	17	48724032	48724193	ABCC3	177	583	17	48724397	48724800

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=88)	Stat. for Synonymous SNVs (# total SNVs=25)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr17:48734459-48734459	p.S134L	4
chr17:48735443-48735443	p.G163S	3
chr17:48753332-48753332	p.A983V	2
chr17:48738339-48738339	p.L288L	2
chr17:48746258-48746258	p.D639N	2
chr17:48750485-48750485	p.V799L	2
chr17:48736616-48736616	p.Y231*	2
chr17:48741452-48741452	p.A440T	2
chr17:48753410-48753410	p.S1009F	2
chr17:48757227-48757227	p.E1258E	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=2

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	9	3	2	14			2		8	1	1	12	3	1			40	10		12
# mutation	9	3	2	13			2		8	1	1	12	3	1			48	11		18
nonsynonymous SNV	6	3	2	10			2		8		1	9	3	1			26	8		11
synonymous SNV	3			3						1		3					22	3		7

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
chr17:48734526	p.A475T,ABCC3	2
chr17:48755478	p.S1009F	2
chr17:48753410	p.P559T	2
chr17:48745263	p.I156I,ABCC3	2
chr17:48742598	p.F1201F	2
chr17:48745836	p.E610K	2
chr17:48753891	p.S1107N	2
chr17:48741448	p.G833D	1
chr17:48750428	p.D27N,ABCC3	1
chr17:48755287	p.T1108A	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 ABCC3 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 ABCC3

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


ABCC2,ABCC3,ANKRD40,C2CD4A,CA10,EPN3,ITGA3, ITGB6,LUC7L3,KAT7,NME1,NME2,NME2P1,NUDT8, PPP1R9B,RTL1,SLC12A3,SLC35B1,SPAG9,TOB1,UTP18	ABCC3,ACTN1,ALOX5,COX6B2,CRB2,DGKA,DSG3, GALNT14,IL34,IL4R,KRT17,KRT5,KRT9,LAMC2, PLCH2,RHBDF2,SFN,TEAD3,TMEM51,TRIM17,UNC13D

ABCC3,PHYKPL,ALS2CL,ARHGAP27,CAPN8,DGKA,EPS8L1, EXD3,FAM83E,KIAA1522,LOC146880,MMP28,MYO7B,OSBPL7, PDZD3,PLCD3,PLEKHM1,PTPRH,TMC4,UGT1A10,VSIG2	ABCC3,PRR14L,CC2D1A,CDH1,CPT1A,ENTPD5,FZD5, GRAMD4,HNF4A,LETM1,MAVS,MFSD9,MINK1,MYO1D, PLCE1,PRSS12,RAPGEFL1,TMEM131,TMEM63B,TRAPPC10,TRPM4

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 ABCC3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00709	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved; investigational	Lamivudine
DB00143	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved; nutraceutical	Glutathione
DB00544	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved	Fluorouracil
DB00145	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved; nutraceutical	Glycine
DB00515	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved	Cisplatin
DB00441	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved	Gemcitabine
DB00158	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved; nutraceutical	Folic Acid
DB00650	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved	Leucovorin
DB00563	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved	Methotrexate
DB00773	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved	Etoposide
DB00444	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved	Teniposide
DB00762	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved; investigational	Irinotecan
DB00987	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved; investigational	Cytarabine
DB00741	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	approved	Hydrocortisone

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Cross referenced IDs for ABCC3

* 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