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 ABCC5

Basic gene info.	Gene symbol	ABCC5
	Gene name	ATP-binding cassette, sub-family C (CFTR/MRP), member 5
	Synonyms	ABC33\|EST277145\|MOAT-C\|MOATC\|MRP5\|SMRP\|pABC11
	Cytomap	UCSC genome browser: 3q27
	Genomic location	chr3 :183701540-183735727
	Type of gene	protein-coding
	RefGenes	NM_001023587.1, NM_005688.2,
	Ensembl id	ENSG00000114770
	Description	ATP-binding cassette sub-family C member 5canalicular multispecific organic anion transporter Cmulti-specific organic anion transporter Cmultidrug resistance-associated protein 5
	Modification date	20141207
dbXrefs	MIM : 605251
	HGNC : HGNC
	Ensembl : ENSG00000114770
	HPRD : 06898
	Vega : OTTHUMG00000156871
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ABCC5
	BioGPS: 10057
	Gene Expression Atlas: ENSG00000114770
	The Human Protein Atlas: ENSG00000114770
Pathway	NCI Pathway Interaction Database: ABCC5
	KEGG: ABCC5
	REACTOME: ABCC5
	ConsensusPathDB
	Pathway Commons: ABCC5
Metabolism	MetaCyc: ABCC5
	HUMANCyc: ABCC5
Regulation	Ensembl's Regulation: ENSG00000114770
	miRBase: chr3 :183,701,540-183,735,727
	TargetScan: NM_001023587
	cisRED: ENSG00000114770
Context	iHOP: ABCC5
	cancer metabolism search in PubMed: ABCC5
	UCL Cancer Institute: ABCC5
Assigned class in ccmGDB	C

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Phenotypic Information for ABCC5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ABCC5
	Familial Cancer Database: ABCC5

* 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_HYALURONAN_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: ABCC5
	MedGen: ABCC5 (Human Medical Genetics with Condition)
	ClinVar: ABCC5
Phenotype	MGI: ABCC5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ABCC5

Mutations for ABCC5

* 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 ABCC5 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
BC007229	ABCC5	1	546	3	183705558	183732135	TGFBI	534	1270	5	135397183	135399507
AW062626	ABCC5	1	100	3	183638354	183638453	TSPAN14	88	149	10	82278551	82278612
CN409264	ABCC5	201	230	3	183643359	183643388	ATN1	231	472	12	7045390	7045631

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=108)	Stat. for Synonymous SNVs (# total SNVs=45)

Stat. for Deletions (# total SNVs=7)	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
chr3:183665257-183665257	p.L1090fs*26	4
chr3:183665244-183665244	p.A1094A	3
chr3:183667646-183667646	p.R1041H	3
chr3:183699516-183699516	p.Q382Q	3
chr3:183665245-183665245	p.A1094V	2
chr3:183689598-183689598	p.S505N	2
chr3:183665250-183665250	p.T1092T	2
chr3:183699560-183699560	p.I368V	2
chr3:183639099-183639099	p.V1435I	2
chr3:183639117-183639117	p.A1429T	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	5	5	1	18	6		5		4	1		16	11	5		1	9	14	1	14
# mutation	5	5	1	20	6		5		4	1		18	15	5		1	9	15	1	23
nonsynonymous SNV	4	4	1	13	3		4		4	1		12	11	3		1	6	12	1	13
synonymous SNV	1	1		7	3		1					6	4	2			3	3		10

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
chr3:183689508	p.H1053N	2
chr3:183700635	p.R535L	2
chr3:183667611	p.V1435I	2
chr3:183639099	p.I1007I	2
chr3:183667837	p.R251Q	2
chr3:183696311	p.A778V	1
chr3:183639187	p.I585I	1
chr3:183665250	p.T1390T	1
chr3:183677612	p.E387E	1
chr3:183700588	p.G1237R	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 ABCC5 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 ABCC5

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


ABCC5,HECTD4,CACNG4,CCDC117,DNAJC14,EIF2B5,EPB41L5, GPRC5A,KIAA0196,KIF3B,CERS6,MARVELD2,MKL2,KAT6B, PIGX,RAB30,SAMD8,SENP2,SIX4,VPS8,WWP1	ABCC5,AURKA,BMP8A,RHPN1-AS1,EZH2,FAM111A,FBXO43, GGA2,KDM2B,KNTC1,MTBP,MYO19,ORC6,OSBP2, RIMKLA,SLC17A9,SYCP2,TRAF5,ZNF251,ZNF589,ZNF7

ABCC5,CCNL1,DVL3,FCHSD1,KIAA1407,L3MBTL1,LOC202181, LOC220729,LOC91316,LPIN3,LY6G5B,NKTR,PHC3,PLXNB1, RPL32P3,SNORA71E,STK36,TTC14,TTLL3,UCKL1-AS1,ZDHHC23	ABCC5,ANKRD36,BDP1,BTAF1,C17orf85,CEP290,CPSF7, DNHD1,FAM156A,LOC202181,MEG3,NKTR,NXF1,OTUD3, PRDM2,RBM5,SFSWAP,SIN3B,TAF1C,ZNF621,ZNF767P

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 ABCC5

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
DB00544	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Fluorouracil
DB01248	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved; investigational	Docetaxel
DB00515	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Cisplatin
DB00441	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Gemcitabine
DB00203	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved; investigational	Sildenafil
DB01033	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Mercaptopurine
DB00352	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Thioguanine
DB00762	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved; investigational	Irinotecan
DB00987	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved; investigational	Cytarabine
DB00741	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Hydrocortisone
DB00650	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Leucovorin
DB00563	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Methotrexate
DB01004	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved; investigational	Ganciclovir
DB00495	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	approved	Zidovudine

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Cross referenced IDs for ABCC5

* 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