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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 NR4A1
check button Gene summary
Basic gene informationGene symbolNR4A1
Gene namenuclear receptor subfamily 4, group A, member 1
SynonymsGFRP1|HMR|N10|NAK-1|NGFIB|NP10|NUR77|TR3
CytomapUCSC genome browser: 12q13
Type of geneprotein-coding
RefGenesNM_001202233.1,
NM_001202234.1,NM_002135.4,NM_173157.2,NM_173158.1,
DescriptionST-59TR3 orphan receptorearly response protein NAK1growth factor-inducible nuclear protein N10hormone receptornerve growth factor IB nuclear receptor variant 1nuclear hormone receptor NUR/77nuclear receptor subfamily 4 group A member 1orphan nucle
Modification date20141222
dbXrefs MIM : 139139
HGNC : HGNC
Ensembl : ENSG00000123358
HPRD : 00744
Vega : OTTHUMG00000150393
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NR4A1
BioGPS: 3164
PathwayNCI Pathway Interaction Database: NR4A1
KEGG: NR4A1
REACTOME: NR4A1
Pathway Commons: NR4A1
ContextiHOP: NR4A1
ligand binding site mutation search in PubMed: NR4A1
UCL Cancer Institute: NR4A1
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)OvarySoft tissue
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)OVSARC
Reference showing the relevant tissue of NR4A1
Description by TissGene annotationsCancer gene
Fused withTSGene
* 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
GO:0002042cell migration involved in sprouting angiogenesis18059339
GO:0045944positive regulation of transcription from RNA polymerase II promoter22427340
GO:0002042cell migration involved in sprouting angiogenesis18059339
GO:0045944positive regulation of transcription from RNA polymerase II promoter22427340


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TissGeneExp for NR4A1

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
KIRP-1.4400030152.45391886-3.8939218754.02E-125.85E-11
LIHC-1.438381640.74862836-2.187012.45E-124.42E-11
THCA0.6084944952.273060597-1.6645661029.20E-073.48E-06
LUAD-0.1203505372.135930498-2.2562810343.04E-132.52E-12
LUSC-0.6872897192.399243615-3.0865333332.89E-172.37E-16
BRCA-1.0380331141.153066009-2.1910991232.79E-202.02E-19
KIRC0.0844827491.576003582-1.4915208334.91E-081.40E-07
BLCA0.0901642543.940769518-3.8506052636.67E-101.24E-07
HNSC-0.701751780.591264499-1.2930162790.001150.003810751


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TissGene-miRNA for NR4A1

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 NR4A1
TissGeneSNV for NR4A1

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.A247PESCA1
p.W482*LUSC1
p.L562MBRCA1
p.L616MSARC1
p.R450HGBM1
p.R569PLUAD1
p.A288PESCA1
p.P377SPAAD1
p.A59VLIHC1
p.R31CSTAD1
p.P28LLIHC1
p.P431SPAAD1
p.L616MLIHC1
p.D412NSKCM1
p.S544*HNSC1
p.A305SLUSC1
p.S245FSKCM1
p.A329VCOAD1
p.D408ECOAD1
p.A288EESCA1
p.G273VLUAD1
p.S492FSKCM1
p.S485NGBM1
p.G172SMESO1
p.V162GPRAD1
p.F146CSTAD1
p.E499DLUAD1
p.P167SSKCM1
p.Q309KTHYM1
p.S191FSKCM1
p.R370QBLCA1
p.F159CSTAD1
p.G611RLIHC1
p.A359DUCEC1
p.A92SLUAD1
p.S546FSKCM1
p.R316*PAAD1
p.P411SSKCM1
p.Q52HLUAD1
p.S201RSTAD1
p.C475YBRCA1
p.L364RSKCM1
p.G219VLUAD1
p.P390SPAAD1
p.R345WPAAD1
p.R316QBLCA1
p.P411LSKCM1
p.I486VUCEC1
p.R18CSTAD1
p.G412VCOAD1
p.D247NKICH1
p.P521LSTAD1
p.P312LCESC1
p.G159SUCEC1
p.A421VUCEC1
p.E135XTHYM1
p.A100VLIHC1
p.R399WBLCA1
p.E389GACC1
p.R315WCOAD1
p.G274DUCS1
p.L418RSKCM1
p.S214RSTAD1
p.G315DUCS1
p.G570RLIHC1
p.V524GLUSC1
p.S385FUCEC1
p.V295ELUSC1
p.L562MUCEC1


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TissGeneCNV for NR4A1

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 NR4A1

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
Chimerdb3.0ChiTaRsNABF928744ANAPC16-NR4A1chr10:73822406chr12:52447594
Chimerdb3.0ChiTaRsNAAW952990AKAP2-NR4A1chr9:112900113chr12:52449648
Chimerdb3.0ChiTaRsNABI909860HNRNPUL2-NR4A1chr11:62489612chr12:52444388
Chimerdb3.0ChiTaRsNABG928171PABPC1-NR4A1chr8:101734059chr12:52451247
Chimerdb3.0ChiTaRsNADB018378CLASP1-NR4A1chr2:122288584chr12:52445226
Chimerdb3.0ChiTaRsNAAW614419SFPQ-NR4A1chr1:35658548chr12:52448107
Chimerdb3.0ChiTaRsNABF915953NR4A1-IFRD2chr12:52451160chr3:50326151
Chimerdb3.0ChiTaRsNABM998971METRN-NR4A1chr16:767480chr12:52452911
Chimerdb3.0ChiTaRsNACD517507TXNL4B-NR4A1chr16:72120192chr12:52446078
Chimerdb3.0ChiTaRsNAAA557827NR4A1-NR4A1chr12:52453057chr12:52452701
Chimerdb3.0ChiTaRsNABI045347PDE9A-NR4A1chr21:44110439chr12:52446067
Chimerdb3.0ChiTaRsNAAV705223NR4A1-NR4A1chr12:52450664chr12:52450284
TCGAfusionPortalPRADAHNSCTCGA-BA-6871-01ANR4A1-IL20RBIn-frameChr12:52435713Chr3:136699308


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TissGeneNet for NR4A1

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)
NR4A1, HSP90B1, NFKB1, MAPK1, CTNNB1, EGR1, SERPINE1, POLA2, MED31, HADHA, EEF1A1, SMARCE1, GLOD4, CPT1A, VPRBP, CHD1L, BBS10, RPL7, ERC1, ZNF331, MYT1L (tumor)NR4A1, HSP90AB1, EGR1, SERPINE1, NCOA2, TERF1, HSPH1, TOP2A, CD2AP, HES1, VASP, NACAD, SMARCC1, SOCS4, SERPING1, ZNF331, MATR3, SEPT4, ESF1, ANKIB1, PCDHGC3 (normal)
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COAD (tumor)COAD (normal)
NR4A1, CHD3, E2F1, MAPK1, GLUD1, MAPK8, EGR1, SERPINE1, MED31, PML, HSPH1, EEF1A1, MYBBP1A, PPM1A, MPDZ, BBS10, RPL7, SOCS4, ZNF331, ESF1, PPBP (tumor)NR4A1, UBC, EGR1, RXRG, SERPINE1, SMARCE1, TOP2A, HES1, VASP, SUGT1, FAF1, ROBO2, BBS10, RPL7, SERPINA4, ZNF331, MATR3, ABCB11, ESF1, PREPL, ABCA5 (normal)
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HNSC (tumor)HNSC (normal)
NR4A1, UBC, YWHAZ, MAPK1, EGR1, TCF4, SERPINE1, POLA2, NCOR2, TOP2A, CD2AP, TMOD3, NACAD, MPDZ, BCL2A1, BBS10, ZNF331, SEPT4, BCL2L10, PCDHGC3, MYT1L (tumor)NR4A1, CHD3, RXRA, EGR1, TCF4, BCL2, TERF1, HADHA, PML, RPS6KA1, CPT1A, TMOD3, RPS6KA6, NACAD, MPDZ, ROBO2, CLU, ABCC6, ZNF331, SEPT4, MYT1L (normal)
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KICH (tumor)KICH (normal)
NR4A1, NR3C1, UBC, YWHAZ, VHL, GK, EGR1, SERPINE1, BCL2, TRIM28, SMARCE1, GLOD4, CD2AP, TMOD3, HES1, VASP, PPM1A, NACAD, ABCG8, ZNF331, ANKIB1 (tumor)NR4A1, NCOA3, SMAD3, STAT3, GK, CHD4, BCL2, CHEK2, ATXN1, SMARCE1, RBL1, MED1, PPM1A, CHD1L, ABCC6, ERC1, ZNF331, ARHGEF5, ANKIB1, PHIP, ABCA5 (normal)
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KIRC (tumor)KIRC (normal)
NR4A1, NR3C1, UBC, CHD3, EGR1, SERPINE1, NCOA2, HADHA, RPS6KA5, HNRNPA2B1, EEF1A1, MYBBP1A, HES1, RPS6KA6, NACAD, PELP1, ABCC6, ZNF331, ARHGEF5, ANKIB1, FXYD3 (tumor)NR4A1, HSP90B1, CTNNB1, EGR1, TCF4, RXRG, POLA2, BCL2, AKT1, CHEK2, RPS6KA1, TOP2A, CPT1A, HES1, PPM1A, ROBO2, BBS10, SOCS4, SERPINA4, ZNF331, PRDX6 (normal)
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KIRP (tumor)KIRP (normal)
NR4A1, HSP90B1, NFKB1, VHL, EGR1, KAT2B, SERPINE1, BCL2, TOP2A, CD2AP, TMOD3, MED1, VPRBP, GADD45GIP1, SMARCC1, ERC1, ZNF331, BCL2L10, ESF1, PCDHGC3, PHIP (tumor)NR4A1, TP53, UBC, RXRA, HIF1A, CHD4, EGR1, NCOA1, TCF4, SERPINE1, NCOR2, RPS6KA5, HES1, BCL2A1, BBS10, ABCC6, ZNF331, SEPT4, BCL2L10, ANKIB1, FXYD3 (normal)
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LIHC (tumor)LIHC (normal)
NR4A1, UBC, VHL, STAT3, MAPK8, EGR1, SERPINE1, PSMC5, TRIM28, MYBBP1A, CPT1A, MTA2, CUTA, TMOD3, SUGT1, FAF1, GADD45GIP1, RPL7, ZNF331, ARHGEF10L, MYT1L (tumor)NR4A1, NR3C1, E2F1, STAT3, GK, EGR1, TCF4, SERPINE1, POLA2, BCL2, TRIM28, TOP2A, CPT1A, HES1, NACAD, SMARCC1, CLU, SERPING1, SEPT4, PPBP, PCDHGC3 (normal)
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LUAD (tumor)LUAD (normal)
NR4A1, SMAD3, PRDX4, MAPK8, EGR1, NCOA1, SERPINE1, NCOA2, EP300, PSMC5, RPS6KA1, GLOD4, CUTA, SUGT1, MPDZ, ROBO2, GADD45GIP1, ERC1, ZNF331, PRDX6, FXYD3 (tumor)NR4A1, RTN4, CHD3, GK, EGR1, SERPINE1, POLA2, HSPH1, ATXN1, TOP2A, RBL1, ALDOC, FAF1, ROBO2, PELP1, CLU, ABCC6, ZNF331, SEPT4, ANKIB1, FXYD3 (normal)
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LUSC (tumor)LUSC (normal)
NR4A1, UBC, RTN4, VHL, EGR1, SERPINE1, POLA2, BCL2, TOP2A, RBL1, GLOD4, TMOD3, PPM1A, SUGT1, CHD1L, BBS10, ZNF331, MATR3, PHIP, ABCA5, LSS (tumor)NR4A1, YWHAZ, CHD3, EGR1, RXRG, SERPINE1, POLA2, NCOR2, MED31, HADHA, FAF1, NACAD, MPDZ, CLU, SERPING1, ABCC6, ZNF331, SEPT4, BCL2L10, PPBP, FXYD3 (normal)
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PRAD (tumor)PRAD (normal)
NR4A1, SMAD3, UBC, CHD3, PRDX4, NFKB1, MAPK1, HDAC6, EGR1, RXRG, SERPINE1, HADHA, HSPH1, HNRNPA2B1, CUTA, HES1, BCL2A1, BBS10, RPL7, ZNF331, ABCA5 (tumor)NR4A1, UBC, YWHAZ, E2F1, VHL, EGR1, RXRG, SERPINE1, PML, HNRNPA2B1, SMARCE1, TOP2A, RBL1, VASP, NACAD, BCL2A1, BBS10, CLU, FABP3, ZNF331, FXYD3 (normal)
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STAD (tumor)STAD (normal)
NR4A1, SMAD3, EGR1, TCF4, RXRG, SERPINE1, BCL2, TERF1, TOP2A, TMOD3, HES1, NACAD, MPDZ, ROBO2, CLU, SERPING1, ZNF331, SEPT4, BCL2L10, PCDHGC3, MYT1L (tumor)NR4A1, UBC, YWHAZ, GLUD1, EGR1, TCF4, RXRG, SERPINE1, CHEK2, HNRNPA2B1, RBL1, SUGT1, RPS6KA6, NACAD, MPDZ, ROBO2, CLU, ZNF331, SEPT4, ESF1, PCDHGC3 (normal)
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THCA (tumor)THCA (normal)
NR4A1, TP53, UBC, YWHAZ, RTN4, EGR1, SERPINE1, TERF1, MED31, HADHA, PML, HSPH1, RPS6KA1, RPS6KA5, HNRNPA2B1, HES1, FABP3, ZNF331, BCL2L10, PPBP, CHMP2B (tumor)NR4A1, UBC, CHD3, SRC, HSP90B1, MAPK1, HDAC6, EGR1, TCF4, SERPINE1, POLA2, PML, CHEK2, RPS6KA1, RPS6KA5, MYBBP1A, GLOD4, ROBO2, ZNF331, PRDX6, SEPT4 (normal)
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TissGeneProg for NR4A1

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 NR4A1
TissGeneDrug for NR4A1

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 NR4A1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0023467Leukemia, Myelocytic, Acute6BeFree,LHGDN
umls:C0007102Malignant tumor of colon4BeFree
umls:C0235974Pancreatic carcinoma4BeFree
umls:C0346647Malignant neoplasm of pancreas4BeFree
umls:C0598766Leukemogenesis4BeFree
umls:C0699790Colon Carcinoma4BeFree
umls:C2239176Liver carcinoma4BeFree
umls:C0003850Arteriosclerosis3BeFree
umls:C0004153Atherosclerosis3BeFree
umls:C0009375Colonic Neoplasms3BeFree,LHGDN
umls:C0023418leukemia3BeFree,LHGDN
umls:C0023434Chronic Lymphocytic Leukemia3BeFree
umls:C0025202melanoma3BeFree,LHGDN
umls:C0038356Stomach Neoplasms3LHGDN
umls:C0596263Carcinogenesis3BeFree
umls:C0009402Colorectal Carcinoma2BeFree
umls:C0021655Insulin Resistance2CTD_human,GAD
umls:C0024299Lymphoma2BeFree,LHGDN
umls:C0026769Multiple Sclerosis2BeFree
umls:C0027627Neoplasm Metastasis2BeFree
umls:C0030297Pancreatic Neoplasm2BeFree
umls:C0376358Malignant neoplasm of prostate2BeFree
umls:C0600139Prostate carcinoma2BeFree
umls:C1332225Aggressive Non-Hodgkin Lymphoma2BeFree
umls:C1458155Mammary Neoplasms2BeFree
umls:C1527249Colorectal Cancer2BeFree
umls:C2939461Myeloid neoplasm2BeFree
umls:C0001486Adenovirus Infections1BeFree
umls:C0003873Rheumatoid Arthritis1BeFree
umls:C0005586Bipolar Disorder1GAD
umls:C0006118Brain Neoplasms1BeFree
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0007134Renal Cell Carcinoma1BeFree
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0011860Diabetes Mellitus, Non-Insulin-Dependent1BeFree,GAD
umls:C0014175Endometriosis1CTD_human
umls:C0015544Failure to Thrive1BeFree
umls:C0019163Hepatitis B1BeFree,LHGDN
umls:C0020443Hypercholesterolemia1BeFree
umls:C0021053Immune System Diseases1BeFree
umls:C0023267Fibroid Tumor1BeFree
umls:C0024121Lung Neoplasms1LHGDN
umls:C0024301Lymphoma, Follicular1BeFree
umls:C0024623Malignant neoplasm of stomach1BeFree
umls:C0025517Metabolic Diseases1BeFree
umls:C0027404Narcolepsy1GAD
umls:C0028754Obesity1BeFree
umls:C0033578Prostatic Neoplasms1LHGDN
umls:C0033805Pseudohypoaldosteronism1BeFree
umls:C0036341Schizophrenia1GAD
umls:C0042133Uterine Fibroids1BeFree
umls:C0042373Vascular Diseases1BeFree
umls:C0079731B-Cell Lymphomas1BeFree
umls:C0079744Diffuse Large B-Cell Lymphoma1BeFree
umls:C0079773Lymphoma, T-Cell, Cutaneous1BeFree
umls:C0085110Severe Combined Immunodeficiency1BeFree
umls:C0085669Acute leukemia1BeFree
umls:C0149521Pancreatitis, Chronic1BeFree
umls:C0151650Renal fibrosis1BeFree
umls:C0151744Myocardial Ischemia1CTD_human
umls:C0152115Lingual-Facial-Buccal Dyskinesia1BeFree,GAD
umls:C0206682Follicular thyroid carcinoma1BeFree
umls:C0242379Malignant neoplasm of lung1BeFree
umls:C0279000Liver and Intrahepatic Biliary Tract Carcinoma1BeFree
umls:C0281361Adenocarcinoma of pancreas1BeFree
umls:C0333186Restenosis1BeFree
umls:C0343457Borderline tuberculoid leprosy1BeFree
umls:C0345904Malignant neoplasm of liver1BeFree
umls:C0376545Hematologic Neoplasms1BeFree
umls:C0549473Thyroid carcinoma1BeFree
umls:C0678222Breast Carcinoma1BeFree
umls:C0684249Carcinoma of lung1BeFree
umls:C0686347Tardive Dyskinesia1GAD
umls:C0686619Secondary malignant neoplasm of lymph node1BeFree
umls:C0699791Stomach Carcinoma1BeFree
umls:C1301355Myelodysplastic-Myeloproliferative Diseases1BeFree
umls:C2004493Leukemia, B-Cell1BeFree