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 RGMB
Gene summary
Basic gene Info.Gene symbolRGMB
Gene namerepulsive guidance molecule family member b
SynonymsDRAGON
CytomapUCSC genome browser: 5q15
Type of geneprotein-coding
RefGenesNM_173670.2,
NM_001012761.2,
DescriptionDRG11-responsive axonal guidance and outgrowth of neuriteRGM domain family member BRGM domain family, member Brepulsive guidance molecule B
Modification date20141207
dbXrefs MIM : 612687
HGNC : HGNC
Ensembl : ENSG00000174136
HPRD : 15243
Vega : OTTHUMG00000162745
ProteinUniProt: Q6NW40
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RGMB
BioGPS: 285704
PathwayNCI Pathway Interaction Database: RGMB
KEGG: RGMB
REACTOME: RGMB
Pathway Commons: RGMB
ContextiHOP: RGMB
ligand binding site mutation search in PubMed: RGMB
UCL Cancer Institute: RGMB
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


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Ligand binding site mutations for RGMB
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
M301V302LCOAD1
M301V302MLUAD1
A300R300HUCEC1
M301V302MUCEC1
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 RGMB
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
(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 RGMB from PDB

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Differential gene expression and gene-gene network for RGMB
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 RGMB and the right PPI network was created from samples without mutations in the LBS of RGMB. 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 RGMB
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0003873Arthritis, Rheumatoid1Biomarker

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

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Pharmacological information for RGMB
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 RGMB go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (PRO,SER,TYR,LEU,PHE,CYS,GLY,LEU,PHE,GLY,ASP)4bq6DA300 M301
IIIPeptide ligand (PRO,SER,TYR,LEU,PHE,CYS,GLY,LEU,PHE,GLY,ASP)4bq6FA300 M301
IIIPeptide ligand (PRO,SER,TYR,LEU,PHE,CYS,GLY,LEU,PHE,GLY,ASP)4bq7DA300 M301
IIIPeptide ligand (PRO,SER,TYR,LEU,PHE,CYS,GLY,LEU,PHE,GLY,ASP)4bq7FA300 M301
IIIPeptide ligand (SER,TYR,LEU,PHE,CYS,GLY,LEU,PHE,GLY,ASP)4bq8CM301


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Conservation information for LBS of RGMB
Multiple alignments for Q6NW40 in multiple species
LBSAA sequence# speciesSpecies


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