mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for PLXNB1
Gene summary
Basic gene Info.Gene symbolPLXNB1
Gene nameplexin B1
SynonymsPLEXIN-B1|PLXN5|SEP
CytomapUCSC genome browser: 3p21.31
Type of geneprotein-coding
RefGenesNM_001130082.2,
NM_002673.5,
Descriptionplexin 5plexin-B1semaphorin receptor SEP
Modification date20141207
dbXrefs MIM : 601053
HGNC : HGNC
Ensembl : ENSG00000164050
HPRD : 03032
Vega : OTTHUMG00000133527
ProteinUniProt: O43157
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLXNB1
BioGPS: 5364
PathwayNCI Pathway Interaction Database: PLXNB1
KEGG: PLXNB1
REACTOME: PLXNB1
Pathway Commons: PLXNB1
ContextiHOP: PLXNB1
ligand binding site mutation search in PubMed: PLXNB1
UCL Cancer Institute: PLXNB1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0007162negative regulation of cell adhesion15218527
GO:0008360regulation of cell shape19843518
GO:0051493regulation of cytoskeleton organization19843518
GO:0071526semaphorin-plexin signaling pathway15218527


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Ligand binding site mutations for PLXNB1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
K1720D1719YCOAD1
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.


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Protein structure related information for PLXNB1
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
K1720D1719Y-0.68994641
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for PLXNB1 from PDB

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Differential gene expression and gene-gene network for PLXNB1
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of PLXNB1 and the right PPI network was created from samples without mutations in the LBS of PLXNB1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for PLXNB1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for PLXNB1
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PLXNB1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK,UNK)3hm6XK1720


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Conservation information for LBS of PLXNB1
Multiple alignments for O43157 in multiple species
LBSAA sequence# speciesSpecies
K1720KHQVDKGPVDS2Homo sapiens, Mus musculus
K1720KHQIEKGLVDA1Drosophila melanogaster
L1923YLTRLLSMKGT2Homo sapiens, Mus musculus
L1923YLTRLLATKGT1Drosophila melanogaster
Q1717RGIKHQVDKGP2Homo sapiens, Mus musculus
Q1717KAIKHQIEKGL1Drosophila melanogaster
T1928LSMKGTLQKFV2Homo sapiens, Mus musculus
T1928LATKGTIQKFV1Drosophila melanogaster


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