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 ITGB2

Gene summary

Basic gene Info.	Gene symbol	ITGB2
	Gene name	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)
	Synonyms	CD18\|LAD\|LCAMB\|LFA-1\|MAC-1\|MF17\|MFI7
	Cytomap	UCSC genome browser: 21q22.3
	Type of gene	protein-coding
	RefGenes	NM_000211.4, NM_001127491.2,NM_001303238.1,
	Description	cell surface adhesion glycoprotein (LFA-1/CR3/P150,959 beta subunit precursor)complement receptor C3 beta-subunitintegrin beta chain, beta 2integrin beta-2leukocyte cell adhesion molecule CD18leukocyte-associated antigens CD18/11A, CD18/11B, CD18/11C
	Modification date	20141222
dbXrefs	MIM : 600065
	HGNC : HGNC
	Ensembl : ENSG00000160255
	HPRD : 02506
	Vega : OTTHUMG00000090257
Protein	UniProt: P05107 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ITGB2
	BioGPS: 3689
Pathway	NCI Pathway Interaction Database: ITGB2
	KEGG: ITGB2
	REACTOME: ITGB2
	Pathway Commons: ITGB2
Context	iHOP: ITGB2
	ligand binding site mutation search in PubMed: ITGB2
	UCL Cancer Institute: ITGB2
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
GO:0007159	leukocyte cell-cell adhesion	12885943
GO:0030593	neutrophil chemotaxis	12885943
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	12885943

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Ligand binding site mutations for ITGB2

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
D264	D264Y	GBM	1
E347	E347Q	LUAD	1
E234	E234Q	LUSC	1
S136,S138	Y137C	STAD	1
D264	D265Y	UCEC	1
D173	K174N	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 ITGB2

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
E347	E347Q	-1.0367909
D173	K174N	-0.641976
S138	Y137C	-0.58011401
S136	Y137C	-0.58011401
D264	D264Y	-0.39233192
D264	D265Y	-0.32408192
E234	E234Q	-0.24121498

(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 ITGB2 from PDB

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Differential gene expression and gene-gene network for ITGB2

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 ITGB2 and the right PPI network was created from samples without mutations in the LBS of ITGB2. 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 ITGB2

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0272187	Congenital leukocyte adherence deficiency	43	Biomarker, GeneticVariation
umls:C0398738	Leukocyte adhesion deficiency type 1	24	Biomarker, GeneticVariation
umls:C0011603	Dermatitis	4	Biomarker
umls:C0023487	Leukemia, Promyelocytic, Acute	3	AlteredExpression, Biomarker
umls:C0032285	Pneumonia	2	Biomarker
umls:C0023510	Leukocyte Disorders	2	Biomarker
umls:C0004943	Behcet Syndrome	1	Biomarker
umls:C0006663	Calcinosis	1	Biomarker
umls:C0263454	Chloracne	1	Biomarker
umls:C0017661	Glomerulonephritis, IGA	1	Biomarker
umls:C0018824	Heart Valve Diseases	1	Biomarker
umls:C0020517	Hypersensitivity	1	Biomarker
umls:C0242597	Leukocyte-Adhesion Deficiency Syndrome	1	Biomarker
umls:C0027720	Nephrosis	1	Biomarker
umls:C0037299	Skin Ulcer	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for ITGB2

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.