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 PAX5

Gene summary

Basic gene Info.	Gene symbol	PAX5
	Gene name	paired box 5
	Synonyms	ALL3\|BSAP
	Cytomap	UCSC genome browser: 9p13
	Type of gene	protein-coding
	RefGenes	NM_001280547.1, NM_001280548.1,NM_001280549.1,NM_001280550.1,NM_001280551.1, NM_001280552.1,NM_001280553.1,NM_001280554.1,NM_001280555.1, NM_001280556.1,NM_016734.2,NR_103999.1,NR_104000.1,
	Description	B-cell lineage specific activatorpaired box homeotic gene 5paired box protein Pax-5paired domain gene 5transcription factor PAX 5
	Modification date	20141212
dbXrefs	MIM : 167414
	HGNC : HGNC
	Ensembl : ENSG00000196092
	HPRD : 01334
	Vega : OTTHUMG00000019907
Protein	UniProt: Q02548 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PAX5
	BioGPS: 5079
Pathway	NCI Pathway Interaction Database: PAX5
	KEGG: PAX5
	REACTOME: PAX5
	Pathway Commons: PAX5
Context	iHOP: PAX5
	ligand binding site mutation search in PubMed: PAX5
	UCL Cancer Institute: PAX5
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_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 PAX5

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
R71	Y72C	BRCA	1
R31	R31Q	COAD	1
R38	V36L	COAD	1
R50	R50M	GBM	1
R31	R31W	GBM	1
S86	S86P	HNSC	1
S131	P130S	HNSC	1
F27	V26G	HNSC	1
A111	A111S	HNSC	1
H62	H62Q	LUAD	1
H62	H62N	LUAD	1
R71	R71M	LUAD	1
W112	E113V	LUAD	1
Q22	L23P	LUSC	1
S131	V129M	UCEC	1
N21	G19R	UCEC	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 PAX5

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
Q22	L23P	-1.625681
F27	V26G	-1.4667496
A111	A111S	-1.347489
R31	R31Q	-1.2376989
S131	V129M	-1.1935078
S131	P130S	-1.0553084
R71	R71M	-1.0516726
R38	V36L	-0.92144073
R31	R31W	-0.90955331
R50	R50M	-0.81823607
R71	Y72C	-0.81106055
N21	G19R	-0.4458523
H62	H62N	-0.44065669
H62	H62Q	-0.34173669
S86	S86P	-0.30683764
W112	E113V	-0.17638073

(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 PAX5 from PDB

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Differential gene expression and gene-gene network for PAX5

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 PAX5 and the right PPI network was created from samples without mutations in the LBS of PAX5. 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 PAX5

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C1961102	Precursor Cell Lymphoblastic Leukemia-Lymphoma	16	Biomarker, GeneticVariation
umls:C0023485	Precursor B-Cell Lymphoblastic Leukemia-Lymphoma	3	Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for PAX5

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 PAX5 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
NUC		Nucleic Acids	1k78	I	A111
NUC		Nucleic Acids	1mdm	A	H62 S86 S131
NUC		Nucleic Acids	1mdm	A	N21 Q22 F27 R31 R38 H62 A111
NUC		Nucleic Acids	1k78	E	N21 Q22 F27 R31 R38 H62 A111 W112
NUC		Nucleic Acids	1k78	A	N21 Q22 F27 R31 R38 H62 R71 S86 A111
NUC		Nucleic Acids	1k78	A	R50 H62 S86 S131
NUC		Nucleic Acids	1k78	E	R50 H62 S86 S131
NUC		Nucleic Acids	1k78	I	S86 S131

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Conservation information for LBS of PAX5

Multiple alignments for Q02548 in multiple species

LBS

AA sequence

# species

Species