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 PEX5
Gene summary
Basic gene Info.Gene symbolPEX5
Gene nameperoxisomal biogenesis factor 5
SynonymsPBD2A|PBD2B|PTS1-BP|PTS1R|PXR1
CytomapUCSC genome browser: 12p13.31
Type of geneprotein-coding
RefGenesNM_000319.4,
NM_001131023.1,NM_001131024.1,NM_001131025.1,NM_001131026.1,
NM_001300789.1,
DescriptionPTS1 receptorperoxin-5peroxisomal C-terminal targeting signal import receptorperoxisomal targeting signal 1 (SKL type) receptorperoxisomal targeting signal 1 receptorperoxisomal targeting signal import receptorperoxisomal targeting signal receptor 1
Modification date20141222
dbXrefs MIM : 600414
HGNC : HGNC
Ensembl : ENSG00000139197
HPRD : 02684
Vega : OTTHUMG00000168175
ProteinUniProt: P50542
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PEX5
BioGPS: 5830
PathwayNCI Pathway Interaction Database: PEX5
KEGG: PEX5
REACTOME: PEX5
Pathway Commons: PEX5
ContextiHOP: PEX5
ligand binding site mutation search in PubMed: PEX5
UCL Cancer Institute: PEX5
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:0006625protein targeting to peroxisome21375735
GO:0016560protein import into peroxisome matrix, docking21976670
GO:0016561protein import into peroxisome matrix, translocation11336669
GO:0051262protein tetramerization12456682
GO:1901094negative regulation of protein homotetramerization21976670


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Ligand binding site mutations for PEX5
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
Y560R559HCOAD1
N568L569FSKCM1
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 PEX5
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
Y560R559H-1.1648284
N568L569F-0.98549778
(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 PEX5 from PDB

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Differential gene expression and gene-gene network for PEX5
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 PEX5 and the right PPI network was created from samples without mutations in the LBS of PEX5. 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 PEX5
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0043459Zellweger Syndrome4Biomarker, GeneticVariation
umls:C3550234PEROXISOME BIOGENESIS DISORDER 2B1Biomarker, GeneticVariation
umls:C0282525Neonatal adrenoleukodystrophy1Biomarker, GeneticVariation

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

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Pharmacological information for PEX5
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 PEX5 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of PEX5
Multiple alignments for P50542 in multiple species
LBSAA sequence# speciesSpecies
A530WNKLGATLANG5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
A533LGATLANGNQS4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
A533LGATLANGNRS1Gallus gallus
D505LSGEYDKAVDC4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
D505LSGEYEKAVDC1Gallus gallus
D509YDKAVDCFTAA4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
D509YEKAVDCFSAA1Gallus gallus
E383TQAENEQELLA5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
E540GNQSEEAVAAY4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
E540GNRSEEAVAAY1Gallus gallus
I564RYNLGISCINL5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
K506SGEYDKAVDCF4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
K506SGEYEKAVDCF1Gallus gallus
K527YLLWNKLGATL3Homo sapiens, Rattus norvegicus, Bos taurus
K527HLLWNKLGATL1Gallus gallus
K527YLMWNKLGATL1Mus musculus
L609WSTLRLALSML4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
L609WSTLRMALSML1Gallus gallus
N415AVSFTNESLQR4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
N415AVSFTNESLQK1Gallus gallus
N499LGVLFNLSGEY5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
N526DYLLWNKLGAT3Homo sapiens, Rattus norvegicus, Bos taurus
N526DHLLWNKLGAT1Gallus gallus
N526DYLMWNKLGAT1Mus musculus
N534GATLANGNQSE4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
N534GATLANGNRSE1Gallus gallus
N561IRSRYNLGISC5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
N568GISCINLGAHR5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
Q537LANGNQSEEAV4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
Q537LANGNRSEEAV1Gallus gallus
R557QPGYIRSRYNL5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
T414LAVSFTNESLQ5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
T531NKLGATLANGN5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
T606ENIWSTLRLAL4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
T606DNIWSTLRMAL1Gallus gallus
V411LMALAVSFTNE5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
V508EYDKAVDCFTA4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
V508EYEKAVDCFSA1Gallus gallus
Y545EAVAAYRRALE5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
Y560YIRSRYNLGIS5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus


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