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Center for Computational Systems Medicine
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Gene Summary

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Translation studies in PubMed

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Exon Skipping Events

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Expression

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Expression Regulation

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Associated Genes

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Protein 3D Structure

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Protein-Protein Interaction

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Mutations

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Prognostic Analysis

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Gender Association

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Age Association

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Related Drugs

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Related Diseases

Translation Factor: TRUB2 (NCBI Gene ID:26995)


Gene Summary

check button Gene Summary
Gene InformationGene Name: TRUB2
Gene ID: 26995
Gene Symbol

TRUB2

Gene ID

26995

Gene NameTruB pseudouridine synthase family member 2
SynonymsCLONE24922
Cytomap

9q34.11

Type of Geneprotein-coding
Descriptionmitochondrial mRNA pseudouridine synthase TRUB2TruB pseudouridine (psi) synthase family member 2TruB pseudouridine (psi) synthase homolog 2probable tRNA pseudouridine synthase 2
Modification date20200313
UniProtAcc

O95900


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of translation
GO:0032543Mitochondrial translation
GO:0045727Positive regulation of translation
GO:0006412Translation


check button Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID


check button Inferred gene age of translation factor.
GeneInferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
TRUB2(733 - 1119.25]


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Translation Studies in PubMed

check button We searched PubMed using 'TRUB2[title] AND translation [title] AND human.'
GeneTitlePMID
TRUB2..


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Exon Skipping Events

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.
all structure

check button Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ENSTExon skip start (DNA)Exon Skip end (DNA)ORF
ENST00000372890131073165131073302Frame-shift
ENST00000372890131076086131076168Frame-shift
ENST00000372890131077845131077907Frame-shift
ENST00000372890131079430131079505In-frame

check button Exon skipping position in the amino acid sequence.
ENSTExon skip start (DNA)Exon Skip end (DNA)Len(transcript seq)Exon skip start (mRNA)Exon Skip end (mRNA)Len(amino acid seq)Exon skip start (AA)Exon Skip end (AA)
ENST00000372890131079430131079505179457665033180105

check button Potentially (partially) lost protein functional features of UniProt.
UniProtAccExon skip start (AA)Exon Skip end (AA)Function feature start (AA)Function feature end (AA)Functional feature typeFunctional feature desc.
O959008010511331ChainID=PRO_0000252090;Note=Mitochondrial mRNA pseudouridine synthase TRUB2
O95900801059898Active siteNote=Nucleophile;Ontology_term=ECO:0000250;evidence=ECO:0000250
O95900801059393Natural variantID=VAR_027749;Note=V->L;Dbxref=dbSNP:rs2072394


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Expression


check buttonGene expression level across TCGA pancancer
all structure

check buttonGene expression level across GTEx pantissue
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check buttonExpression level of gene isoforms across TCGA pancancer
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check buttonExpression level of gene isoforms across GTEx pantissue
all structure

check buttonCancer(tissue) type-specific expression level of Translation factor using z-score distriution
all structure

check buttonDifferential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)
all structure
Cancer typeTranslation factorFCadj.pval
KICHTRUB2-2.061549427115770.00882232189178467
ESCATRUB2-1.630554916195490.0185546875
CHOLTRUB2-2.30701675175370.02734375
BRCATRUB2-2.532797560689831.7326162077773e-13
LUSCTRUB2-3.504733788015461.91629083762368e-08
LUADTRUB2-1.929838020306233.47524877088934e-09


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue


check buttonTranslation factor expression regulation through methylation in the promoter of Translation factor
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through copy number variation of Translation factor
Cancer typeGeneCoefficientPvalue
CESCTRUB2-0.0487015260.00434935
PCPGTRUB20.1425402810.013314385
TGCTTRUB20.0941447430.047161805

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with TRUB2 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)
all structure
Cancer typeGene groupTranslation factorCorrelated geneCoefficientPvalue
DLBCCell metabolism geneTRUB2ANP32A0.8048007225.45E-12
DLBCCell metabolism geneTRUB2SNRPE0.8168678971.44E-12
DLBCCell metabolism geneTRUB2NME10.8190184481.13E-12
DLBCCell metabolism geneTRUB2ATP5G10.8192663441.10E-12
DLBCCell metabolism geneTRUB2TIMM130.8195217721.06E-12
DLBCCell metabolism geneTRUB2SNRPD10.8217331918.22E-13
DLBCCell metabolism geneTRUB2TOMM400.8231076526.99E-13
DLBCCell metabolism geneTRUB2TIMM500.8329290272.10E-13
DLBCCell metabolism geneTRUB2SNRPD30.8474461763.07E-14
DLBCCell metabolism geneTRUB2PMPCA0.876648563.21E-16
DLBCEpifactorTRUB2ANP32A0.8048007225.45E-12
DLBCEpifactorTRUB2RUVBL20.8316809782.46E-13
DLBCTSGTRUB2ANP32A0.8048007225.45E-12
DLBCTSGTRUB2NME10.8190184481.13E-12
DLBCTSGTRUB2PHB0.8381284871.08E-13
KICHCell metabolism geneTRUB2PMPCA0.803402589.52E-22
KICHCell metabolism geneTRUB2PSMB70.814874428.58E-23
THYMCell metabolism geneTRUB2EXOSC50.8010732571.62E-28
THYMCell metabolism geneTRUB2PSMB40.8022126211.19E-28
THYMCell metabolism geneTRUB2PSMD40.8052645755.16E-29
THYMCell metabolism geneTRUB2TOMM400.8079457152.45E-29
THYMCell metabolism geneTRUB2PMPCA0.8106947731.13E-29
THYMCell metabolism geneTRUB2NME10.8117833268.24E-30
THYMCell metabolism geneTRUB2GEMIN70.8156845912.66E-30
THYMCell metabolism geneTRUB2GEMIN60.8212767535.00E-31
THYMEpifactorTRUB2EXOSC50.8010732571.62E-28
THYMTSGTRUB2NME10.8117833268.24E-30
UCSCell metabolism geneTRUB2EXOSC50.8010732571.62E-28
UCSCell metabolism geneTRUB2PSMB40.8022126211.19E-28
UCSCell metabolism geneTRUB2PSMD40.8052645755.16E-29
UCSCell metabolism geneTRUB2TOMM400.8079457152.45E-29
UCSCell metabolism geneTRUB2PMPCA0.8106947731.13E-29
UCSCell metabolism geneTRUB2NME10.8117833268.24E-30
UCSCell metabolism geneTRUB2GEMIN70.8156845912.66E-30
UCSCell metabolism geneTRUB2GEMIN60.8212767535.00E-31
UCSEpifactorTRUB2EXOSC50.8010732571.62E-28
UCSTSGTRUB2NME10.8117833268.24E-30


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Protein structure


check button Protein 3D structure
Visit iCn3D.


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Protein-Protein Interaction


check button Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))
all structure

check buttonOverlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))
all structure
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* Edge colors based on TCGA cancer types.

check button* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))
all structure
Cancer typeTranslation factorInteracting protein coding geneFCadj.pval
KICHTRUB2WBSCR161.52309768216160.000162303447723389
HNSCTRUB2PUS72.635278155529090.000182808133786239
STADTRUB2GAR1-5.072796043067570.000433447770774365
STADTRUB2WBSCR16-1.138338611089840.000433447770774365
LIHCTRUB2DDX28-1.805569199493780.00268062725366399
PRADTRUB2PUS7L1.555705899559180.00430343371125972
ESCATRUB2GAR1-2.388070370103770.0048828125
HNSCTRUB2YARS21.517585047975140.00498432417884942
BLCATRUB2PUS7L-1.936782736366330.00823211669921875
STADTRUB2RPUSD4-1.777596280226720.0148032568395138
UCECTRUB2GAR11.761608525987190.015625
ESCATRUB2YARS2-2.007106844669740.0185546875
LIHCTRUB2FASTKD2-2.174264985089780.0264015241133303
KIRPTRUB2DDX281.787291563384220.0309218638576567
STADTRUB2DDX28-1.744733132806930.0309218638576567
HNSCTRUB2FASTKD2-1.722193451887510.0410440647583528
KIRCTRUB2RPUSD31.030101034001791.09375608261512e-08
PRADTRUB2PUS7-2.665430669490931.37654470439417e-07
HNSCTRUB2RPUSD4-3.648231712562131.42088565553422e-05
LUSCTRUB2WBSCR16-2.870435442768941.86041017272598e-07
LIHCTRUB2PUS7-1.368299946781792.71217975233539e-06
KICHTRUB2GAR1-2.28339493463532.98023223876953e-07
LUADTRUB2WBSCR16-2.845059154008313.09848396407815e-08
PRADTRUB2NGRN-1.954463306829213.16187259327918e-07
KIRPTRUB2PUS7-1.20385077594783.54335643351078e-05
BRCATRUB2PUS7L1.855006868843993.75312800430837e-08
BRCATRUB2FASTKD2-1.956593680899064.12639478109604e-08
KICHTRUB2DDX282.681666750301714.54187393188476e-05
STADTRUB2PUS7-5.060743024105984.5965425670147e-06
THCATRUB2PUS71.247738385190764.88626066707067e-07
KIRCTRUB2PUS7-2.055345296801495.48040034437071e-11
LUSCTRUB2GAR1-2.52986323332589.38793721862767e-08
KIRCTRUB2RPUSD4-3.434567489130049.61177113723533e-08


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with TRUB2
ICT1, Ybx1, LIN28B, HIST1H1A, TRA2A, ZC3H3, MRPL4, HNRNPA1, FYCO1, YARS2, ACAD8, DCAF10, MRPL39, RBMX, MRPS30, OLFM4, HNRNPU, MRPL50, Fus, TRUB2, SPATA20, WBSCR16, BOLA1, UQCC1, UQCC2, NME6, FTH1, MTERF3, CLPX, CLPB, MRPS35, PITRM1, POLDIP2, C17orf89, CYCS, PMPCB, NRD1, ECH1, TIMM50, NGRN, FASTKD2, RBM42, DDX28, LAMP2, HSPD1, ZNF324B, CDX1, FBXW11, C1orf85, PCBP1, SNRNP70, CUL7, DUSP1, GRB2, AUH, C12orf65, C6orf203, CS, GFM1, GRSF1, HINT2, LRPPRC, MDH2, METTL17, MRPL11, MRPS12, MRPS26, MRRF, MTIF2, MTIF3, MTRF1, PMPCA, SSBP1, TACO1, TBRG4, ABCB7, ACAD9, ACADM, ACAT1, ACOT1, ACOT2, AFG3L2, AK4, ALAS1, ALDH2, ALDH4A1, ANGEL2, ATP5B, ATP5D, ATP5E, ATP5J2-PTCD1, ATP5L, ATP5F1, ATP5H, ATP5J, ATP5O, ATPAF1, BCS1L, C17orf80, CARS2, CDK5RAP1, COQ5, COX2, COX4I1, COX5A, DAP3, DBT, DHTKD1, DHX30, DLAT, DLST, DNAJA3, EARS2, ECHS1, ECSIT, EIF2AK2, ELAC2, ERAL1, ETFA, ETFB, FASTKD1, FASTKD5, FECH, FLAD1, GADD45GIP1, GATB, GCDH, GLS, GLUD1, GTPBP10, GTPBP3, GTPBP6, GUF1, HADH, HADHA, HARS2, HIST1H1E, HNRNPA2B1, HNRNPA3, HNRNPAB, HNRNPDL, HNRNPK, HNRNPL, HNRNPR, HNRNPUL1, HSD17B10, HSDL2, HSPE1, IARS2, IBA57, IGF2BP2, ILF3, IVD, KIAA0391, LARS2, LETM1, LONP1, LYRM4, ME2, METTL15, MMAB, RNMTL1, MRPL1, MRPL10, MRPL12, MRPL13, MRPL14, MRPL15, MRPL16, MRPL17, MRPL18, MRPL19, MRPL2, MRPL20, MRPL21, MRPL22, MRPL23, MRPL24, MRPL27, MRPL28, MRPL3, MRPL30, MRPL32, MRPL35, MRPL37, MRPL38, MRPL40, MRPL41, MRPL42, MRPL43, MRPL44, MRPL45, MRPL46, MRPL47, MRPL48, MRPL49, MRPL51, MRPL52, MRPL53, MRPL55, MRPL57, MRPL9, MRPS10, MRPS11, MRPS14, MRPS16, MRPS17, MRPS18A, MRPS18B, MRPS18C, MRPS2, MRPS21, MRPS22, MRPS23, MRPS24, MRPS25, MRPS27, MRPS28, MRPS31, MRPS33, MRPS34, MRPS36, MRPS5, MRPS6, MRPS7, MRPS9, MTO1, MTPAP, NARS2, NDUFA12, NDUFA2, NDUFA5, NDUFA6, NDUFA7, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NDUFV3, NFS1, NIPSNAP1, NME4, NNT, NOA1, NT5DC2, NUBPL, NUDT19, OGDH, OXA1L, PAM16, PDHA1, PDHB, PDHX, PDK1, PDK3, PDPR, PHB, PHB2, PNPLA8, PNPT1, POLG, POLRMT, PPIF, PREPL, PTCD3, PYCR1, PYCR2, QRSL1, RPUSD3, RPUSD4, RTN4IP1, ACN9, SDHB, SHMT2, SLC30A9, SLIRP, SRSF10, SRSF3, SRSF9, STOML2, SUCLA2, SUPV3L1, TFAM, THEM4, TIMM44, TRA2B, TRMT10C, TRMT61B, TSFM, C10orf2, VARS2, VWA8, FASN, DDX39A, YBX1, CBX6, HNRNPUL2, IGF2BP3, UTP23, NUPL2, MSI1, RBM47, PTCD1, RNF7, FAM120A, YBX2, PRR3, MAP7, RBMS2, UQCRFS1, SRSF7, FAHD1, MARS2, RPS2, MCAT, GPR45, APOBEC3D, LIN28A, SRSF6, RPS19, ZNF346, PAIP1, ABT1, RBMS3, ZC3HAV1, RPL31, NEIL1, ILF2, PABPC5, MICB, MALSU1,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
TRUB2chr9131071922CTsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
TRUB2chr9131084628CTsingle_nucleotide_variantLikely_benignnot_providedSO:0001819|synonymous_variant,SO:0001623|5_prime_UTR_variantSO:0001819|synonymous_variant,SO:0001623|5_prime_UTR_variant


check button nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.
all structure


check button SNVs and Indels
GeneCancer typeChromosomeStartEndRefSeeqMutSeqMutation typeAAchange# samples
TRUB2CESCchr9131071960131071960GCMissense_Mutationp.Q289E3
TRUB2HNSCchr9131084583131084583CGSilentp.L35L3
TRUB2CESCchr9131071960131071960GCMissense_Mutation3
TRUB2CESCchr9131072039131072039GASilent2
TRUB2SKCMchr9131071999131071999GASilentp.L276L2
TRUB2KIRCchr9131071988131071988GCMissense_Mutationp.I279M2
TRUB2CESCchr9131073194131073194GASilent2
TRUB2KIRCchr9131072107131072107GAMissense_Mutationp.H240Y2
TRUB2CESCchr9131072104131072104CGMissense_Mutationp.E241Q2
TRUB2STADchr9131077859131077859GTMissense_Mutationp.A122D2
TRUB2LGGchr9131072049131072049CTMissense_Mutationp.R259H2
TRUB2UCECchr9131073848131073848GASilentp.L1652
TRUB2UCECchr9131076118131076118CAMissense_Mutationp.E143D2
TRUB2LGGchr9131072049131072049CTMissense_Mutation2
TRUB2PAADchr9131083973131083973CTMissense_Mutationp.R49H2
TRUB2HNSCchr9131073208131073208CAMissense_Mutationp.G210C2
TRUB2BRCAchr9131073254131073254CASilentp.V1942
TRUB2LIHCchr9131072114131072114CTSilent2
TRUB2CESCchr9131072104131072104CGMissense_Mutation2
TRUB2PRADchr9131071863131071863GCMissense_Mutationp.S321C2
TRUB2CESCchr9131079472131079472CTMissense_Mutation2
TRUB2KIRCchr9131071913131071913GTSilentp.T304T2
TRUB2THCAchr9131076114131076114CAMissense_Mutation2
TRUB2KIRCchr9131072072131072072GCSilentp.V251V2
TRUB2LIHCchr9131071972131071972C-Frame_Shift_Delp.A286fs1
TRUB2DLBCchr9131073842131073842CTMissense_Mutationp.V167I1
TRUB2LUADchr9131071839131071839GAMissense_Mutationp.A329V1
TRUB2HNSCchr9131073208131073208CAMissense_Mutation1
TRUB2SKCMchr9131073167131073167TAMissense_Mutationp.L223F1
TRUB2CESCchr9131079489131079489GASilent1
TRUB2LUADchr9131073868131073868CTMissense_Mutationp.R158K1
TRUB2HNSCchr9131084583131084583CGSilent1
TRUB2SKCMchr9131073167131073167TASplice_Sitep.L223_splice1
TRUB2BLCAchr9131072029131072029CTMissense_Mutation1
TRUB2KIRPchr9131073210131073210GCMissense_Mutationp.T209S1
TRUB2LUADchr9131071861131071861TCMissense_Mutationp.T322A1
TRUB2HNSCchr9131076091131076091GTSilent1
TRUB2STADchr9131079460131079460CTMissense_Mutationp.R96Q1
TRUB2BLCAchr9131073221131073221CASilent1
TRUB2KIRPchr9131072155131072155CASplice_Site1
TRUB2OVchr9131071899131071899CTMissense_Mutationp.S309N1
TRUB2HNSCchr9131076091131076091GTSilentp.T152T1
TRUB2BLCAchr9131072029131072029CTMissense_Mutationp.D266N1
TRUB2CESCchr9131071960131071960GANonsense_Mutationp.Q289*1
TRUB2PAADchr9131083973131083973CTMissense_Mutation1
TRUB2STADchr9131076121131076121AGSilentp.R142R1
TRUB2BLCAchr9131073221131073221CASilentp.P205P1
TRUB2CESCchr9131072039131072039GASilentp.F2621
TRUB2STADchr9131071975131071975GAMissense_Mutationp.R284W1
TRUB2LIHCchr9131076148131076148GTSilent1
TRUB2CESCchr9131079472131079472CTMissense_Mutationp.G92D1
TRUB2PCPGchr9131077879131077879GASilent1
TRUB2HNSCchr9131084698131084698CASplice_Site1
TRUB2STADchr9131079460131079460CTMissense_Mutation1
TRUB2CESCchr9131073194131073194GASilentp.L2141
TRUB2KIRCchr9131077879131077879GASilentp.L115L1
TRUB2STADchr9131072106131072106TCMissense_Mutation1
TRUB2LIHCchr9131076096131076096TCMissense_Mutationp.T151A1
TRUB2COADchr9131072127131072127TCMissense_Mutationp.K233R1
TRUB2PRADchr9131073259131073259CTMissense_Mutationp.A193T1
TRUB2LIHCchr9131072114131072114CTSilentp.K237K1
TRUB2COADchr9131079488131079488CTMissense_Mutationp.A87T1
TRUB2SARCchr9131073290131073290GTSilent1
TRUB2THYMchr9131072048131072048GTSilent1

check buttonCopy number variation (CNV) of TRUB2
* Click on the image to open the original image in a new window.
all structure

check buttonFusion gene breakpoints (product of the structural variants (SVs)) across TRUB2
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


check button Fusion genes with this translation factor from FusionGDB2.0.
FusionGDB2 IDDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
80464N/ABM972018DNAH10chr12124372252-TRUB2chr9131071388+
80464OVTCGA-09-2045-01AEXOC4chr7133164892+TRUB2chr9131079505-
80464READTCGA-DY-A1DFSEPT10chr2110303626-TRUB2chr9131084009-
94471N/AEC485729TRUB2chr9131074402+BEAN1chr1666522827-
94471N/AAK130008TRUB2chr9131084189-EHD2chr1948225937+
94471BLCATCGA-GD-A3OSTRUB2chr9131083877-KCNT1chr9138641943+
94471BLCATCGA-GD-A3OS-01ATRUB2chr9131083878-KCNT1chr9138641944+
94471ESCATCGA-L5-A4OSTRUB2chr9131083877-MAPKAP1chr9128348006-
94471N/ACB050626TRUB2chr9131071388-PALB2chr1623642204+
98474N/ABU623091TRUB2chr9131075838+TAPBPchr633269249+


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Prognostic Analysis


check button Kaplan-Meier plots with logrank tests of overall survival (OS)
all structure
Cancer typeTranslation factorCoefficentHazard ratioWald test pvalLikelihool ratio pvalLogrank test pval# samples


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Translation factor and Gender


check button Differential gene expression between female and male. (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
LUADTRUB20.008898042502508770.25
LGGTRUB20.01443367570793390.39
LIHCTRUB20.0167998457000630.44
HNSCTRUB20.02222349198939730.56
KIRPTRUB20.02421556377816610.58

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Translation factor and Age


check button Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
LUSCTRUB20.002481138575764130.079
THCATRUB20.0001916507882320540.0063
CESCTRUB20.0093015955214170.29
ESCATRUB20.04131434981545821

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Related Drugs


check button Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases


check button Diseases associated with this translation factor.
(DisGeNet 4.0)
Disease IDDisease Name# PubMedsDisease source