mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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	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 PEX3

Gene summary

Basic gene Info.	Gene symbol	PEX3
	Gene name	peroxisomal biogenesis factor 3
	Synonyms	PBD10A\|TRG18
	Cytomap	UCSC genome browser: 6q24.2
	Type of gene	protein-coding
	RefGenes	NM_003630.2,
	Description	peroxin-3peroxisomal assembly protein PEX3transformation-related protein 18
	Modification date	20141219
dbXrefs	MIM : 603164
	HGNC : HGNC
	HPRD : 04407
Protein	UniProt: P56589 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PEX3
	BioGPS: 8504
Pathway	NCI Pathway Interaction Database: PEX3
	KEGG: PEX3
	REACTOME: PEX3
	Pathway Commons: PEX3
Context	iHOP: PEX3
	ligand binding site mutation search in PubMed: PEX3
	UCL Cancer Institute: PEX3
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID

GO Term

PubMed ID

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Ligand binding site mutations for PEX3

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

LBS	AAchange of nsSNV	Cancer type	# samples
T90	S88N	BLCA	1
K197	H198R	HNSC	1

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 PEX3

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.

LBS	AAchange of nsSNV	Relative stability change
T90	S88N	-1.3347246
K197	H198R	-0.16501184

(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 PEX3 from PDB

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Differential gene expression and gene-gene network for PEX3

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 PEX3 and the right PPI network was created from samples without mutations in the LBS of PEX3. 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 PEX3

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0043459	Zellweger Syndrome	7	Biomarker, GeneticVariation
umls:C1832200	Peroxisome biogenesis disorders	3	Biomarker
umls:C3553999	PEROXISOME BIOGENESIS DISORDER 10A (ZELLWEGER)	1	GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for PEX3

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 status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PEX3 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
III		Peptide ligand (ALA,ASP,ARG,GLU,LEU,GLU,GLU,LEU,LEU,GLU,SER,ALA,LEU,ASP,ASP,PHE,ASP)	3mk4	A	K197
III		Peptide ligand (ASP,ARG,GLU,LEU,GLU,GLU,LEU,LEU,GLU,SER,ALA,LEU,ASP,ASP,PHE,ASP,LYS,ALA,LYS,PRO,SER,PRO,ALA,PRO,PRO,SER)	3ajb	A	T90 K197

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Conservation information for LBS of PEX3

Multiple alignments for P56589 in multiple species

LBS	AA sequence	# species	Species
A323	VSLPLAKIIPI	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
A323	DAPSQKFQVAL	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
A323	---QQQYQMAV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A323	--SKNSYQIAL	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
A323	--MQLAKLLPQ	1	Arabidopsis thaliana
A323	--KPLAKVLPQ	1	Arabidopsis thaliana
H334	VNGQIHSVCSE	3	Homo sapiens, Mus musculus, Rattus norvegicus
H334	YSVALKDCCQE	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H334	FAMSMKDCCQE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H334	FSIATKDCTNE	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
H334	INGQIHSVCSE	1	Bos taurus
H334	IEKTMPEISAE	1	Arabidopsis thaliana
H334	IEKTMNVITAE	1	Arabidopsis thaliana
K100	-----KLEIWE	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
K100	TVARSKAELWQ	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
K100	SPLKSKAELWN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K100	TSTKSKAELWD	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
K100	-----KLQLWN	1	Arabidopsis thaliana
K100	-----KLQLWD	1	Arabidopsis thaliana
K197	GSVSLKHSLSL	3	Homo sapiens, Mus musculus, Bos taurus
K197	GTLSPRDTLSM	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
K197	DGIHPRDTLTL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K197	QNSNPRDIMTM	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
K197	GSISLKHSLSL	1	Rattus norvegicus
K197	KGKQLKDVLTT	1	Arabidopsis thaliana
K197	KGKQLKDVITT	1	Arabidopsis thaliana
K324	SLPLAKIIPIV	3	Homo sapiens, Mus musculus, Rattus norvegicus
K324	APSQKFQVALY	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
K324	--QQQYQMAVF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K324	-SKNSYQIALF	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
K324	SLPLAKIIPII	1	Bos taurus
K324	-MQLAKLLPQI	1	Arabidopsis thaliana
K324	-KPLAKVLPQI	1	Arabidopsis thaliana
K94	LTALLKN----	2	Homo sapiens, Rattus norvegicus
K94	LVETLKGKKL-	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
K94	IVTQLKDQKNQ	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K94	IVEALKGKKLQ	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
K94	LTALLKS----	1	Mus musculus
K94	LTALLKT----	1	Bos taurus
K94	IMDKLSKGKGI	1	Arabidopsis thaliana
K94	VMDRLNQGKGM	1	Arabidopsis thaliana
L107	EIWEDLKIISF	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
L107	ELWQELKMRSA	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L107	ELWNELELKSL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L107	ELWDDLKLKAI	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L107	QLWNELKILSF	1	Arabidopsis thaliana
L107	QLWDELKILSF	1	Arabidopsis thaliana
L196	LGSVSLKHSLS	3	Homo sapiens, Mus musculus, Bos taurus
L196	FGTLSPRDTLS	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L196	FDGIHPRDTLT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L196	FQNSNPRDIMT	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L196	LGSISLKHSLS	1	Rattus norvegicus
L196	LKGKQLKDVLT	1	Arabidopsis thaliana
L196	LKGKQLKDVIT	1	Arabidopsis thaliana
L93	SLTALLKN---	2	Homo sapiens, Rattus norvegicus
L93	ELVETLKGKKL	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L93	SIVTQLKDQKN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L93	SIVEALKGKKL	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L93	SLTALLKS---	1	Mus musculus
L93	SLTALLKT---	1	Bos taurus
L93	SIMDKLSKGKG	1	Arabidopsis thaliana
L93	HVMDRLNQGKG	1	Arabidopsis thaliana
P321	SSVSLPLAKII	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
P321	AADAPSQKFQV	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
P321	-----QQQYQM	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P321	DI--SKNSYQI	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
P321	----MQLAKLL	1	Arabidopsis thaliana
P321	----KPLAKVL	1	Arabidopsis thaliana
P327	LAKIIPIVNGQ	3	Homo sapiens, Mus musculus, Rattus norvegicus
P327	QKFQVALYSVA	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
P327	QQYQMAVFAMS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P327	NSYQIALFSIA	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
P327	LAKIIPIINGQ	1	Bos taurus
P327	LAKLLPQIEKT	1	Arabidopsis thaliana
P327	LAKVLPQIEKT	1	Arabidopsis thaliana
T90	NSESLTALLKN	2	Homo sapiens, Rattus norvegicus
T90	DVEELVETLKG	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
T90	NLDSIVTQLKD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T90	DLDSIVEALKG	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
T90	NSESLTALLKS	1	Mus musculus
T90	NSESLTALLKT	1	Bos taurus
T90	DVSSIMDKLSK	1	Arabidopsis thaliana
T90	DVSHVMDRLNQ	1	Arabidopsis thaliana
W104	-KLEIWEDLKI	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
W104	SKAELWQELKM	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
W104	SKAELWNELEL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
W104	SKAELWDDLKL	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
W104	-KLQLWNELKI	1	Arabidopsis thaliana
W104	-KLQLWDELKI	1	Arabidopsis thaliana