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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for ABCB4
check button Gene summary
Basic gene informationGene symbolABCB4
Gene nameATP-binding cassette, sub-family B (MDR/TAP), member 4
SynonymsABC21|GBD1|ICP3|MDR2|MDR2/3|MDR3|PFIC-3|PGY3
CytomapUCSC genome browser: 7q21.1
Type of geneprotein-coding
RefGenesNM_000443.3,
NM_018849.2,NM_018850.2,
DescriptionATP-binding cassette sub-family B member 4P glycoprotein 3/multiple drug resistance 3P-glycoprotein 3P-glycoprotein-3/multiple drug resistance-3multidrug resistance protein 3multiple drug resistance 3
Modification date20141207
dbXrefs MIM : 171060
HGNC : HGNC
Ensembl : ENSG00000005471
HPRD : 01371
Vega : OTTHUMG00000023396
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ABCB4
BioGPS: 5244
PathwayNCI Pathway Interaction Database: ABCB4
KEGG: ABCB4
REACTOME: ABCB4
Pathway Commons: ABCB4
ContextiHOP: ABCB4
ligand binding site mutation search in PubMed: ABCB4
UCL Cancer Institute: ABCB4
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesHPA,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Liver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHC
Reference showing the relevant tissue of ABCB4
Description by TissGene annotationsFused withOncogene
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for ABCB4

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
KIRC0.735725603-0.8357493971.5714752.03E-117.70E-11
KICH-3.204955786-0.928439786-2.2765161.27E-086.65E-08
LUAD-1.118172338-2.7510792341.6329068976.39E-113.91E-10
LIHC5.4255722146.760088214-1.3345160.0006120.001747111
KIRP0.815855464-0.5023007861.318156250.0004980.001463324
HNSC-2.019733926-0.932206019-1.0875279070.0003290.001282929
BLCA-1.851575786-0.14444947-1.7071263162.35E-050.000370667


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TissGene-miRNA for ABCB4

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for ABCB4
TissGeneSNV for ABCB4

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.G90ESKCM3
p.E1150KSKCM2
p.S615RPRAD1
p.E888XCOAD1
p.W708*UCEC1
p.V336FSTAD1
p.R144XCOAD1
p.L1212VBLCA1
p.P105SSKCM1
p.R549LHNSC1
p.T815SSKCM1
p.D682YLUSC1
p.S696FSKCM1
p.X1287RSTAD1
p.G880EBLCA1
p.I1133MOV1
p.P551TLUAD1
p.F210LTHYM1
p.R13CSTAD1
p.T524ACOAD1
p.R361TBLCA1
p.S483PUCEC1
p.P95SREAD1
p.A601TSTAD1
p.R144XSKCM1
p.R212TLUSC1
p.N91HUCEC1
p.W1114XSTAD1
p.V465ILUAD1
p.K7NUCEC1
p.W854XTHYM1
p.E1106DUCEC1
p.E470KSKCM1
p.Y492CSARC1
p.A6TGBM1
p.S339XCOAD1
p.G762RHNSC1
p.R913KSKCM1
p.A542TSTAD1
p.T583NSKCM1
p.Q678*HNSC1
p.G622VBLCA1
p.C353SLUAD1
p.T560MOV1
p.R595QPAAD1
p.L1016VCESC1
p.V713MMESO1
p.L817HLIHC1
p.S136LSKCM1
p.L856SSTAD1
p.K1258NLUAD1
p.S951FSKCM1
p.G495ESKCM1
p.G1179ESKCM1
p.E172KSKCM1
p.V713MLGG1
p.A254TGBM1
p.L533QLUAD1
p.C1073RLUAD1
p.S666THNSC1
p.M790TSTAD1
p.R144*SKCM1
p.M516ISKCM1
p.T593MCOAD1
p.R47XSTAD1
p.G1074ESKCM1
p.Q823HUCEC1
p.T61ISTAD1
p.R545HKIRC1
p.R159*LUAD1
p.V906ILGG1
p.A1047VSKCM1
p.E616KREAD1
p.D180VOV1
p.R957XSKCM1
p.E275*UCEC1
p.I866MESCA1
p.L123FLUSC1
p.S765FLIHC1
p.D972YUCEC1
p.L644QSTAD1
p.L55FSTAD1
p.R1194*STAD1
p.I637LUCEC1
p.G1255ALUAD1
p.F85LSTAD1
p.F154VUCEC1
p.G126ESKCM1
p.G79EESCA1
p.G163VACC1
p.F463CESCA1
p.T1232NLUAD1
p.A1090VSTAD1
p.E22QBLCA1
p.D449NBLCA1
p.G714RSKCM1
p.K1156NUCEC1
p.G612RGBM1
p.R957*BLCA1
p.L701MHNSC1
p.E1215KCESC1
p.L627ILUAD1
p.R549CBLCA1
p.I377NSTAD1
p.R957QUCEC1
p.T828ALGG1
p.K672NCOAD1
p.W1114*STAD1
p.M968TLUAD1
p.G1032RSKCM1
p.R47*STAD1
p.L218FLUAD1
p.I108FUCEC1
p.E616KSKCM1
p.E901KUCEC1
p.R785KBLCA1
p.E901*UCEC1
p.R1174*UCEC1
p.E1215KLUAD1
p.D564EACC1
p.K1060TLUAD1
p.E1165KUCS1
p.G966ALUAD1
p.V712ITHYM1
p.T1092AUCEC1
p.R1046QHNSC1
p.G24RLGG1
p.R545HUCEC1
p.K32ESTAD1
p.V347ILIHC1
p.R147MUCEC1
p.R797ILUSC1
p.K793EKIRP1
p.R788WUCEC1
p.K1218EOV1
p.C433YLUSC1
p.I839LLUAD1
p.Q423RLGG1
p.D576GOV1
p.L1025PSTAD1
p.R13HSTAD1
p.L314MSTAD1
p.L1081RSTAD1
p.G1032ESKCM1
p.V526GBRCA1
p.R47QUCEC1
p.R1046QCOAD1
p.S436GSTAD1
p.E513VLUSC1
p.S300YUCEC1
p.G392ESKCM1
p.G1054RKIRP1
p.L73FREAD1
p.E4QCESC1
p.R47QESCA1
p.E1058QSKCM1
p.A204THNSC1
p.R957*SKCM1
p.E528KHNSC1
p.G9RLUSC1
p.A252TUCEC1
p.E707XREAD1
p.A222VPRAD1
p.Y365HGBM1
p.E901KUCS1
p.I763NLUAD1
p.R1144WBLCA1
p.E49*UCEC1
p.A141TCESC1
p.D744NBRCA1
p.F754LUCEC1
p.P95SSKCM1
p.G163*LUAD1
p.S1132NUCEC1
p.K552NSTAD1
p.V985ACOAD1
p.D459YHNSC1
p.E470KCOAD1
p.T15MLGG1
p.L518SUCEC1
p.R957*CESC1
p.D799GPAAD1
p.M795IGBM1
p.R406*HNSC1
p.L771RUCEC1
p.D50NUCEC1
p.G714RLUSC1
p.D449NHNSC1
p.S69LBLCA1
p.R47*UCEC1
p.Q772*SKCM1
p.N808YUCEC1
p.D564NLGG1
p.Q749LLIHC1
p.K244RSKCM1
p.A833VSARC1


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TissGeneCNV for ABCB4

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for ABCB4

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0TopHat-FusionSARCTCGA-FX-A3RE-01AABCB4-ABCB1In-Framechr7:87035693chr7:87138716
TCGAfusionPortalPRADAHNSCTCGA-CR-6467-01AABCC4-ABCB4In-frameChr13:95829961Chr7:87038708


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TissGeneNet for ABCB4

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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COAD (tumor)COAD (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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HNSC (tumor)HNSC (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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KICH (tumor)KICH (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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KIRC (tumor)KIRC (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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KIRP (tumor)KIRP (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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LIHC (tumor)LIHC (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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LUAD (tumor)LUAD (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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LUSC (tumor)LUSC (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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PRAD (tumor)PRAD (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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STAD (tumor)STAD (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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THCA (tumor)THCA (normal)
ABCB4, HAX1, TESK1, PIGY (tumor)ABCB4, HAX1, TESK1, PIGY (normal)
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TissGeneProg for ABCB4

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for ABCB4
TissGeneDrug for ABCB4

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for ABCB4

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0268312Progressive intrahepatic cholestasis (disorder)30BeFree,CTD_human
umls:C0268318Cholestasis of pregnancy25BeFree,CTD_human,ORPHANET
umls:C0008370Cholestasis20BeFree,GAD,RGD
umls:C2609268Low phospholipid-associated cholelithiasis15BeFree,CTD_human,MGD,ORPHANET,UNIPROT
umls:C0008372Intrahepatic Cholestasis13BeFree,GAD,LHGDN
umls:C0023895Liver diseases13BeFree,GAD,LHGDN
umls:C0008350Cholelithiasis11BeFree,GAD,LHGDN
umls:C1865643Cholestasis, progressive familial intrahepatic 39BeFree,CLINVAR,CTD_human,MGD,ORPHANET,UNIPROT
umls:C0008312Primary biliary cirrhosis8BeFree
umls:C0023434Chronic Lymphocytic Leukemia7BeFree
umls:C0023892Biliary cirrhosis7BeFree,CTD_human,GAD,LHGDN
umls:C0856727Cholesterol gallstones7BeFree
umls:C2239176Liver carcinoma7BeFree,CTD_human,MGD
umls:C0023890Liver Cirrhosis6BeFree,CTD_human
umls:C0947622Cholecystolithiasis5BeFree,GAD
umls:C0008313Cholangitis, Sclerosing4BeFree,CTD_human,GAD
umls:C0023418leukemia4BeFree
umls:C1623038Cirrhosis4BeFree
umls:C0032962Pregnancy Complications3GAD
umls:C0033774Pruritus3BeFree,GAD
umls:C0239946Fibrosis, Liver3BeFree
umls:C0566602Primary sclerosing cholangitis3BeFree,MGD
umls:C0860204Cholestatic liver disease3BeFree
umls:C1512409Hepatocarcinogenesis3BeFree
umls:C3554241CHOLESTASIS, INTRAHEPATIC, OF PREGNANCY 33CLINVAR,UNIPROT
umls:C0019159Hepatitis A2BeFree
umls:C0021368Inflammation2CTD_human,GAD
umls:C0023486Prolymphocytic Leukemia2BeFree
umls:C0023903Liver neoplasms2BeFree
umls:C0029925Ovarian Carcinoma2BeFree
umls:C0031117Peripheral Neuropathy2BeFree,CTD_human
umls:C0085605Liver Failure2BeFree
umls:C0085669Acute leukemia2BeFree
umls:C0242216Biliary calculi2LHGDN
umls:C0745744End Stage Liver Disease2BeFree,CTD_human
umls:C1140680Malignant neoplasm of ovary2BeFree
umls:C1279296Chronic leukemia (category)2BeFree
umls:C0005586Bipolar Disorder1BeFree
umls:C0006118Brain Neoplasms1BeFree
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0008311Cholangitis1CTD_human
umls:C0008354Cholera1BeFree
umls:C0008626Congenital chromosomal disease1BeFree
umls:C0009404Colorectal Neoplasms1CTD_human
umls:C0010068Coronary heart disease1GAD
umls:C0010674Cystic Fibrosis1BeFree,GAD
umls:C0011853Diabetes Mellitus, Experimental1RGD
umls:C0014556Epilepsy, Temporal Lobe1GAD
umls:C0016059Fibrosis1GAD
umls:C0021655Insulin Resistance1GAD
umls:C0022354Jaundice, Obstructive1CTD_human
umls:C0023449Acute lymphocytic leukemia1BeFree
umls:C0026764Multiple Myeloma1BeFree
umls:C0027819Neuroblastoma1BeFree
umls:C0035412Rhabdomyosarcoma1BeFree
umls:C0079588Ichthyosis, X-Linked1BeFree
umls:C0149841Benign recurrent intrahepatic cholestasis1BeFree
umls:C0242379Malignant neoplasm of lung1BeFree
umls:C0242656Disease Progression1CTD_human
umls:C0278996Cancer of Head and Neck1BeFree
umls:C0280248stage, chronic lymphocytic leukemia1BeFree
umls:C0341439Chronic liver disease1BeFree
umls:C0400966Non-alcoholic Fatty Liver Disease1BeFree,CTD_human
umls:C0524909Hepatitis B, Chronic1BeFree
umls:C0524910Hepatitis C, Chronic1BeFree
umls:C0678222Breast Carcinoma1BeFree
umls:C0684249Carcinoma of lung1BeFree
umls:C0700095Central neuroblastoma1BeFree
umls:C0742395Cholestasis, chronic1BeFree
umls:C0746102Chronic lung disease1BeFree
umls:C0796149Scott Syndrome1BeFree
umls:C1263666Advanced cirrhosis1BeFree
umls:C1290807Diarrheal disorder1BeFree
umls:C1621958Glioblastoma Multiforme1BeFree
umls:C3489789Cholestasis, Progressive Familial Intrahepatic, 21BeFree
umls:C3805083Portal fibrosis1BeFree
umls:C0008325Cholecystitis0CLINVAR