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 ABCC3
Basic gene info.Gene symbolABCC3
Gene nameATP-binding cassette, sub-family C (CFTR/MRP), member 3
SynonymsABC31|EST90757|MLP2|MOAT-D|MRP3|cMOAT2
CytomapUCSC genome browser: 17q22
Genomic locationchr17 :48712217-48769063
Type of geneprotein-coding
RefGenesNM_001144070.1,
NM_003786.3,NM_020037.1,NM_020038.1,
Ensembl idENSG00000108846
DescriptionATP-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 date20141207
dbXrefs MIM : 604323
HGNC : HGNC
Ensembl : ENSG00000108846
HPRD : 06826
Vega : OTTHUMG00000162245
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ABCC3
BioGPS: 8714
Gene Expression Atlas: ENSG00000108846
The Human Protein Atlas: ENSG00000108846
PathwayNCI Pathway Interaction Database: ABCC3
KEGG: ABCC3
REACTOME: ABCC3
ConsensusPathDB
Pathway Commons: ABCC3
MetabolismMetaCyc: ABCC3
HUMANCyc: ABCC3
RegulationEnsembl's Regulation: ENSG00000108846
miRBase: chr17 :48,712,217-48,769,063
TargetScan: NM_001144070
cisRED: ENSG00000108846
ContextiHOP: ABCC3
cancer metabolism search in PubMed: ABCC3
UCL Cancer Institute: ABCC3
Assigned class in ccmGDBC

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Phenotypic Information for ABCC3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ABCC3
MedGen: ABCC3 (Human Medical Genetics with Condition)
ClinVar: ABCC3
PhenotypeMGI: ABCC3 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasABCC3chr174876045448760474chr201293510812935128
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ABCC3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW450940ERCC6L21321199877664498776842ABCC3207390174873808848738271
AK000791ABCC312578174876688348769460ABCC325723327174876552348766278
BQ302632ABCC320377174876095248761501DLGAP2366400814568001506271
AI761355YWHAZ11908101951468101951657ABCC3188273174872133848721423
AI905457ABCC320182174872403248724193ABCC3177609174872439748724829
AI905516ABCC320182174872403248724193ABCC3177583174872439748724800

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample10     2          
GAIN (# sample)10     2          
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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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=4

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check002.gifSomatic 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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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
chr17:48734459-48734459p.S134L4
chr17:48735443-48735443p.G163S3
chr17:48753332-48753332p.A983V2
chr17:48738339-48738339p.L288L2
chr17:48746258-48746258p.D639N2
chr17:48750485-48750485p.V799L2
chr17:48736616-48736616p.Y231*2
chr17:48741452-48741452p.A440T2
chr17:48753410-48753410p.S1009F2
chr17:48757227-48757227p.E1258E2

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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
# sample93214  2 8111231  4010 12
# mutation93213  2 8111231  4811 18
nonsynonymous SNV63210  2 8 1931  268 11
synonymous SNV3  3     1 3    223 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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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
chr17:48734526p.A475T,ABCC32
chr17:48755478p.S1009F2
chr17:48753410p.P559T2
chr17:48745263p.I156I,ABCC32
chr17:48742598p.F1201F2
chr17:48745836p.E610K2
chr17:48753891p.S1107N2
chr17:48741448p.G833D1
chr17:48750428p.D27N,ABCC31
chr17:48755287p.T1108A1

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 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

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

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
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 ABCC3
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
DB00709ATP-binding cassette, sub-family C (CFTR/MRP), member 3approved; investigationalLamivudine
DB00143ATP-binding cassette, sub-family C (CFTR/MRP), member 3approved; nutraceuticalGlutathione
DB00544ATP-binding cassette, sub-family C (CFTR/MRP), member 3approvedFluorouracil
DB00145ATP-binding cassette, sub-family C (CFTR/MRP), member 3approved; nutraceuticalGlycine
DB00515ATP-binding cassette, sub-family C (CFTR/MRP), member 3approvedCisplatin
DB00441ATP-binding cassette, sub-family C (CFTR/MRP), member 3approvedGemcitabine
DB00158ATP-binding cassette, sub-family C (CFTR/MRP), member 3approved; nutraceuticalFolic Acid
DB00650ATP-binding cassette, sub-family C (CFTR/MRP), member 3approvedLeucovorin
DB00563ATP-binding cassette, sub-family C (CFTR/MRP), member 3approvedMethotrexate
DB00773ATP-binding cassette, sub-family C (CFTR/MRP), member 3approvedEtoposide
DB00444ATP-binding cassette, sub-family C (CFTR/MRP), member 3approvedTeniposide
DB00762ATP-binding cassette, sub-family C (CFTR/MRP), member 3approved; investigationalIrinotecan
DB00987ATP-binding cassette, sub-family C (CFTR/MRP), member 3approved; investigationalCytarabine
DB00741ATP-binding cassette, sub-family C (CFTR/MRP), member 3approvedHydrocortisone


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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



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