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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 UPB1
check button Gene summary
Basic gene informationGene symbolUPB1
Gene nameureidopropionase, beta
SynonymsBUP1
CytomapUCSC genome browser: 22q11.2
Type of geneprotein-coding
RefGenesNM_016327.2,
Descriptionbeta-alanine synthasebeta-ureidopropionasen-carbamoyl-beta-alanine amidohydrolase
Modification date20141217
dbXrefs MIM : 606673
HGNC : HGNC
Ensembl : ENSG00000100024
HPRD : 09451
Vega : OTTHUMG00000150749
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UPB1
BioGPS: 51733
PathwayNCI Pathway Interaction Database: UPB1
KEGG: UPB1
REACTOME: UPB1
Pathway Commons: UPB1
ContextiHOP: UPB1
ligand binding site mutation search in PubMed: UPB1
UCL Cancer Institute: UPB1
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)KidneyLiver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)KIRC,KIRP,KICHLIHC
Reference showing the relevant tissue of UPB1
Description by TissGene annotationsProtective TissGene in RFS
Significant down-regulated DEG
TissgsKTS
CNV lost TissGeneKTS
Fused withOncogene
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


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TissGeneExp for UPB1

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
KIRP1.3089617556.553530505-5.244568752.98E-146.96E-13
KICH-0.507225625.32163038-5.8288565.38E-136.70E-12
LUSC-0.520972131.471280811-1.9922529411.20E-136.17E-13
LUAD-0.335068311.413478242-1.7485465521.07E-151.17E-14
LIHC8.8940683810.59148638-1.6974180.0001080.000371888


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TissGene-miRNA for UPB1

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 UPB1
TissGeneSNV for UPB1

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.R155CSKCM2
p.R101QSKCM2
p.R266WSKCM2
p.R326QSKCM1
p.D309EOV1
p.P178SSKCM1
p.E137QBLCA1
p.R168WHNSC1
p.V95GSKCM1
p.A278SSTAD1
p.A4VSTAD1
p.R236WHNSC1
p.N206KBLCA1
p.R227KSKCM1
p.E207KUCEC1
p.P88LSKCM1
p.D267YLUAD1
p.T359AKIRC1
p.K32RUCEC1
p.R159KSKCM1
p.G303RCOAD1
p.R220*SKCM1
p.I192VUCS1
p.Q65XSTAD1
p.F44LLIHC1
p.E45KUCEC1
p.E45KSKCM1
p.S232LBLCA1
p.Q65*STAD1
p.F57YSKCM1
p.P183SSKCM1
p.G235RSTAD1
p.W20*UCEC1
p.S300LBLCA1
p.R31CBLCA1
p.R31HSTAD1
p.S187FUCEC1
p.S8LSKCM1
p.S324NUCEC1
p.W286*SKCM1
p.Q166*SKCM1
p.E271KUCEC1
p.V72AKIRP1
p.H97RUCEC1
p.R17HPAAD1
p.R150HBRCA1
p.L133FOV1
p.V38MSKCM1
p.Q308HREAD1
p.A87VUCEC1
p.R326QREAD1
p.F125YSKCM1
p.I260VUCS1
p.A102DPAAD1
p.R169QSKCM1
p.E137AUCEC1
p.N138KBLCA1
p.R334WSKCM1
p.A285VSKCM1
p.H162YSKCM1
p.S179FSKCM1
p.E69QBLCA1
p.A217VSKCM1
p.V28IPAAD1
p.V74MSTAD1
p.R68QSKCM1
p.H237YTHYM1
p.G75ELUAD1


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TissGeneCNV for UPB1

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 UPB1

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
TCGAfusionPortalPRADAHNSCTCGA-CX-7086-01ABCR-UPB1CDS-5UTRChr22:23524426Chr22:24890077


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TissGeneNet for UPB1

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)


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TissGeneProg for UPB1

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 UPB1
TissGeneDrug for UPB1

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 UPB1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C1291512Beta-Ureidopropionase Deficiency3BeFree,CLINVAR,CTD_human,ORPHANET,UNIPROT
umls:C0004352Autistic Disorder1CTD_human
umls:C0009404Colorectal Neoplasms1GAD
umls:C0025517Metabolic Diseases1CTD_human
umls:C0037769West Syndrome1CTD_human