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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: PLXNB2 (NCBI Gene ID:23654)


Gene Summary

check button Gene Summary
Gene InformationGene Name: PLXNB2
Gene ID: 23654
Gene Symbol

PLXNB2

Gene ID

23654

Gene Nameplexin B2
SynonymsMM1|Nbla00445|PLEXB2|dJ402G11.3
Cytomap

22q13.33

Type of Geneprotein-coding
Descriptionplexin-B2
Modification date20200313
UniProtAcc

O15031


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of 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
HgenePLXNB2

GO:0007156

homophilic cell adhesion via plasma membrane adhesion molecules

16122393

HgenePLXNB2

GO:0010976

positive regulation of neuron projection development

16122393



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


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Translation Studies in PubMed

check button We searched PubMed using 'PLXNB2[title] AND translation [title] AND human.'
GeneTitlePMID
PLXNB2..


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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
ENST000004491035071527050715335Frame-shift
ENST000003593375071527050715335Frame-shift
ENST000003593375071805850718205In-frame
ENST000004491035071805850718205In-frame
ENST000004491035071843350718500Frame-shift
ENST000003593375071843350718500Frame-shift
ENST000003593375072061250720742Frame-shift
ENST000004491035072061250720742Frame-shift
ENST000003593375072147850721615Frame-shift
ENST000004491035072147850721615Frame-shift
ENST000003593375072256050722642Frame-shift
ENST000004491035072256050722642Frame-shift
ENST000004491035072300150723094In-frame
ENST000003593375072300150723094In-frame
ENST000004491035072422850724330In-frame
ENST000003593375072422850724330In-frame
ENST000003593375072553950725693Frame-shift
ENST000004491035072553950725693Frame-shift
ENST000003593375072609550726222Frame-shift
ENST000004491035072609550726222Frame-shift
ENST0000044910350727945507290263UTR-3CDS
ENST0000035933750727945507290263UTR-3CDS
ENST0000035933750733147507332073UTR-3UTR
ENST0000044910350733154507332073UTR-3UTR

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)
ENST000003593375071805850718205636843524498183814141463
ENST000004491035071805850718205640043844530183814141463
ENST0000035933750723001507230946368219822901838696727
ENST0000044910350723001507230946400223023221838696727
ENST0000035933750724228507243306368209621971838662696
ENST0000044910350724228507243306400212822291838662696

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.
O15031696727201838ChainID=PRO_0000024673;Note=Plexin-B2
O1503114141463201838ChainID=PRO_0000024673;Note=Plexin-B2
O15031662696201838ChainID=PRO_0000024673;Note=Plexin-B2
O15031696727201838ChainID=PRO_0000024673;Note=Plexin-B2
O1503114141463201838ChainID=PRO_0000024673;Note=Plexin-B2
O15031662696201838ChainID=PRO_0000024673;Note=Plexin-B2
O15031696727201197Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15031662696201197Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15031696727201197Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15031662696201197Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
O150311414146312191838Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
O150311414146312191838Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
O150311414146314621469Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4E71
O150311414146314621469Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4E71


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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
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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
STADPLXNB21.07042195281280.0093395933508873
THCAPLXNB22.686054285050587.49003326178242e-10


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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
all structure
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a
KIRCPLXNB2320.01345055540921750.6493857319182390.572006688596491-0.51675882088348-0.643346824855674
LUADPLXNB2320.02691004186470710.6674518834252450.5685035156250010.0731777107481380.244407122512773

check buttonTranslation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)
all structure
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a
UCECPLXNB2320.045050795099380.6874644076120320.550965057471265-0.560184839674956-0.958049871109493

check buttonTranslation factor expression regulation through copy number variation of Translation factor
all structure
Cancer typeGeneCoefficientPvalue
PCPGPLXNB2-0.0889964480.027117153

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with PLXNB2 (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
THYMCell metabolism genePLXNB2PISD0.828108685.99E-32
THYMCell metabolism genePLXNB2AGRN0.8421374085.63E-34
THYMCell metabolism genePLXNB2FKBP90.8125928616.53E-30
THYMCell metabolism genePLXNB2UGGT20.8245040981.85E-31
THYMCell metabolism genePLXNB2SDC40.8309883082.38E-32
THYMCGCPLXNB2FKBP90.8125928616.53E-30
THYMCGCPLXNB2ZNRF30.8272649677.82E-32
THYMCGCPLXNB2SDC40.8309883082.38E-32
THYMIUPHARPLXNB2LTBR0.8179669161.35E-30
THYMIUPHARPLXNB2PISD0.828108685.99E-32
THYMIUPHARPLXNB2ITGA30.8419190666.08E-34
THYMIUPHARPLXNB2MMP140.8103478291.24E-29
THYMIUPHARPLXNB2CAPN20.8059383394.28E-29
THYMTFPLXNB2KLF110.8235739752.47E-31
UCSCell metabolism genePLXNB2AGRN0.8421374085.63E-34
UCSCell metabolism genePLXNB2SDC40.8309883082.38E-32
UCSCell metabolism genePLXNB2PISD0.828108685.99E-32
UCSCell metabolism genePLXNB2UGGT20.8245040981.85E-31
UCSCell metabolism genePLXNB2FKBP90.8125928616.53E-30
UCSCGCPLXNB2ZNRF30.8272649677.82E-32
UCSCGCPLXNB2SDC40.8309883082.38E-32
UCSCGCPLXNB2FKBP90.8125928616.53E-30
UCSIUPHARPLXNB2PISD0.828108685.99E-32
UCSIUPHARPLXNB2LTBR0.8179669161.35E-30
UCSIUPHARPLXNB2ITGA30.8419190666.08E-34
UCSIUPHARPLXNB2MMP140.8103478291.24E-29
UCSIUPHARPLXNB2CAPN20.8059383394.28E-29
UCSTFPLXNB2KLF110.8235739752.47E-31


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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
LUSCPLXNB2RND31.048182539155720.000102202753672845
BLCAPLXNB2RND3-1.469946983513530.000335693359375
KICHPLXNB2SEMA3E1.265839350973580.00115483999252319
LUADPLXNB2ARHGEF12-1.296937341563830.00121089428940613
THCAPLXNB2SEMA3E1.722265651867680.00146528750243568
COADPLXNB2RRAS-1.309580809843560.00160405039787293
STADPLXNB2SEMA3E-1.558294722926720.00275033386424184
COADPLXNB2SEMA4F-1.001241807441740.00322914123535157
KICHPLXNB2RND32.604389440998540.00378090143203735
COADPLXNB2SEMA3F-2.449178460777690.00390031933784485
CHOLPLXNB2SEMA4F-4.453452265812990.00390625
CHOLPLXNB2RND3-3.503602385135780.00390625
CHOLPLXNB2SEMA4D-1.653558505615950.0078125
CHOLPLXNB2ARHGEF12-3.549861180903840.0078125
BRCAPLXNB2SEMA4F-1.23139244692950.00820001368943606
ESCAPLXNB2SEMA4F-4.46306401077670.013671875
ESCAPLXNB2MET1.79740427610420.0185546875
KIRPPLXNB2ARHGEF11-2.935328390449730.0194480954669416
CHOLPLXNB2RND1-1.128341793477830.01953125
COADPLXNB2RND3-1.031085708311060.0381683111190796
CHOLPLXNB2SEMA3F-1.279133031818790.0390625
LIHCPLXNB2SEMA4F-1.464340469938991.09871251804152e-08
KIRCPLXNB2SEMA4D-1.337324177505271.29783194913552e-06
THCAPLXNB2RRAS2.553908212238371.34811402718136e-08
KIRCPLXNB2SEMA3F2.058432362588471.44148329893084e-11
THCAPLXNB2MET2.090202687093971.50904867455457e-10
KIRCPLXNB2SEMA3E2.087933055155751.55238188425888e-10
HNSCPLXNB2SEMA3E4.226907140320521.99774895008887e-05
KICHPLXNB2SEMA3F1.636604776093472.5629997253418e-06
LUSCPLXNB2SEMA3F2.631531162677943.32807340670689e-07
LIHCPLXNB2SEMA3E3.88235388669853.59406613648813e-06
LUADPLXNB2RRAS-4.229344150464063.59910232594763e-11
LUSCPLXNB2ARHGEF12-4.312877932865583.85129646231505e-08
LIHCPLXNB2ARHGEF12-1.415072557279654.08456474127691e-05
KIRPPLXNB2ARHGEF12-1.021348845874134.20957803726197e-07
PRADPLXNB2MET1.646435288579844.53264387257039e-06
KIRPPLXNB2MET1.520402099134284.6566128730774e-10
LIHCPLXNB2RND3-4.685147465103524.91907449309094e-09
BRCAPLXNB2SEMA3F1.851240943726125.1639316957333e-15
LIHCPLXNB2ARHGEF11-3.849844420301225.1965939338348e-08
LUADPLXNB2SEMA3E-1.098279690059276.23590787285683e-08
LIHCPLXNB2SEMA3F-1.803783851044227.79049220721842e-10
KICHPLXNB2MET1.182062500716488.34465026855468e-07
PRADPLXNB2RRAS-2.030946248904168.40517570249428e-09
LUSCPLXNB2SEMA4F2.027550158505799.88885026766033e-06


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with PLXNB2
ARHGEF11, RND1, PTN, ARHGEF12, PLCG1, HMOX2, CENPU, PFDN1, C12orf57, TACC1, NIF3L1, FBXO6, CCDC8, RHOD, PVRIG, HLA-E, LMAN2, BTNL8, PTCH1, PTPRK, SIAE, LYPD6, NTRK1, TMX1, DEFA1, DEFA5, ST8SIA4, IL17RC, TMED6, SCGB1D1, ADAM21, TLR1, IL27RA, MPPE1, TMPRSS3, TRIM25, PTPRO, RNF4, GRB2, KIAA1429, VDAC2, VDAC3, APEX1, LMBR1L, FAM105A, PLEKHA4, E, M, nsp4, nsp6, ORF7a, ORF7b, ORF8, ST7, RET, FKBP8, SEC61B, E5a, E5b, DNAJC1, DNAJC25, ARF6, ATP2A1, CYP2C9, DERL1, DHFRL1, ELOVL5, EMD, HSD17B11, HSD3B7, KRAS, LAMP2, LAMP3, KIAA1715, LRRC59, LYN, MARCKS, METTL7A, RAB2A, RAB35, RAB5C, RAB9A, RPN1, RPN2, SEC62, SSR1, SMAD4, EDDM3B, LGALS1, PATE1, LY86, RNF149, SLC22A3, FBXO2, ZDHHC12, SEMA4C, SCGB2A1, KLRC1, CDHR3, C2CD4B, CRYZL1, C7orf34, CLEC12B, BTNL3, C1orf54, RLN1, CYHR1, APOA2, CD160, SERGEF, DEFB135, SPCS1, PIGH, TRGV3, BRICD5, ASIC4, IGLL5, SDF2L1, CST11, CLEC2B, IL5RA, DNASE1L1, SLURP1, TMEM106A, CNTNAP3, GGH, HLA-G, TSHR, ECEL1, SFTPC, CBLN4, BTNL2, DPP4, TMPRSS11B, TMPRSS4, TMPRSS2, TMEM106B,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
PLXNB2chr2250719833GAsingle_nucleotide_variantLikely_benignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
PLXNB2chr2250719860CTsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
PLXNB2chr2250720295GAsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variant,SO:0001627|intron_variantSO:0001819|synonymous_variant,SO:0001627|intron_variant
PLXNB2chr2250721296GAsingle_nucleotide_variantBenignnot_providedSO:0001583|missense_variantSO:0001583|missense_variant
PLXNB2chr2250722277CTsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
PLXNB2chr2250725640CTsingle_nucleotide_variantLikely_benignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
PLXNB2chr2250727512GAsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
PLXNB2chr2250728168GAsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_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

check buttonCopy number variation (CNV) of PLXNB2
* 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 PLXNB2
* 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
95424ESCATCGA-IG-A97HCPSF6chr1269656342+PLXNB2chr2250727571-
95424N/ABF087400KRT7chr1252638511+PLXNB2chr2250713901-
98934N/AEC558010PLXNB2chr2250734803-DARSchr2136664836+
102928READTCGA-F5-6814PLXNB2chr2250733148-DENND6Bchr2250757432-
100995BRCATCGA-AN-A0FV-01APLXNB2chr2250733148-DLG2chr1183691685-
89789KIRPTCGA-P4-A5EBPLXNB2chr2250722030-MAST4chr566195778+
89789KIRPTCGA-P4-A5EB-01APLXNB2chr2250722031-MAST4chr566195779+
92253N/AAA984189PLXNB2chr2250723783-MERTKchr2112783070-
81726KIRCTCGA-CZ-5460-01APLXNB2chr2250724229-NDUFA4L2chr1257631118-
70674N/AAV688404PLXNB2chr2250713413-NKAIN1chr131685909-
86557PRADTCGA-J9-A52B-01APLXNB2chr2250713408-P4HTMchr349038871+
66578N/AAA532612PLXNB2chr2250713408-PAK6chr1540536625-
95424N/ABI033029PLXNB2chr2250730363+PLXNB2chr2250730429-
81444STADTCGA-BR-7722-01APLXNB2chr2250724229-PRMT1chr1950191419+
101174N/ABM979599PLXNB2chr2250713472+RBM25chr1473586932-
80746STADTCGA-BR-A4PE-01APLXNB2chr2250745982-RPL23chr1737008985-
66578LGGTCGA-TM-A84JPLXNB2chr2250721479-SMPD4P1chr2220968022-
66578LGGTCGA-TM-A84J-01APLXNB2chr2250721766-SMPD4P1chr2220968022-
98981CESCTCGA-VS-A9V0-01APLXNB2chr2250718434-ST3GAL1chr8134511432-
98320LUADTCGA-55-7913-01BPLXNB2chr2250713408-SUPT16Hchr1421829491-
66578UCECTCGA-AJ-A3EMPLXNB2chr2250733147-TMPRSS6chr2237499458-
66578UCECTCGA-AJ-A3EM-01APLXNB2chr2250733148-TMPRSS6chr2237499458-
66578UCECTCGA-AJ-A3EM-01APLXNB2chr2250745982-TMPRSS6chr2237499458-
102670N/AAI492115PLXNB2chr2250713479+TRIM25chr1754990919+
99580LUADTCGA-75-7031-01APLXNB2chr2250713408-UTRNchr6144665237+
95424STADTCGA-BR-A4PD-01ARNF213chr1778354727+PLXNB2chr2250721195-
95424BRCATCGA-AR-A1AQ-01ASBF1chr2250899952-PLXNB2chr2250723094-
95424BRCATCGA-E2-A1L7-01ASHANK3chr2251160865+PLXNB2chr2250733207-
95424BRCATCGA-E2-A1L7-01ASHANK3chr2251160865-PLXNB2chr2250729026-
95424N/AAI964040TACC1chr838710310-PLXNB2chr2250728748+
95424HNSCTCGA-BA-A4IFTAF9chr568665483-PLXNB2chr2250717440-
95425OVTCGA-13-1403TUBGCP6chr2250678632-PLXNB2chr2250723094-
95425OVTCGA-13-1403-01ATUBGCP6chr2250678633-PLXNB2chr2250723094-
95425UCECTCGA-EO-A22X-01ATUBGCP6chr2250682148-PLXNB2chr2250723094-


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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
TGCTPLXNB20.001260959833618460.035
LUADPLXNB20.01376896970844920.37
BRCAPLXNB20.01745448433328660.45

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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
LIHCPLXNB20.03968981489407911
LUSCPLXNB20.0006350474863401520.021
GBMPLXNB20.007918242485172450.23
LGGPLXNB20.002335910449309480.072
LAMLPLXNB20.008360556873012630.23
ESCAPLXNB20.0237734015591220.64
THYMPLXNB20.001551524201339880.05
SARCPLXNB20.003411842878802420.1

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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