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 HLA-DQA1

Gene summary

Basic gene Info.	Gene symbol	HLA-DQA1
	Gene name	major histocompatibility complex, class II, DQ alpha 1
	Synonyms	CD\|CELIAC1\|DQ-A1\|GSE\|HLA-DQA
	Cytomap	UCSC genome browser: 6p21.3
	Type of gene	protein-coding
	RefGenes	NM_002122.3,
	Description	DC-1 alpha chainDC-alphaHLA class II histocompatibility antigen, DQ alpha 1 chainHLA class II histocompatibility antigen, DQ(W3) alpha chainHLA-DCAMHC HLA-DQ alphaMHC class II DQA1MHC class II HLA-D alpha glycoproteinMHC class II HLA-DQ-alpha-1MH
	Modification date	20141222
dbXrefs	MIM : 146880
	HGNC : HGNC
	Ensembl : ENSG00000196735
	HPRD : 06765
	Vega : OTTHUMG00000031106
Protein	UniProt: P01909 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HLA-DQA1
	BioGPS: 3117
Pathway	NCI Pathway Interaction Database: HLA-DQA1
	KEGG: HLA-DQA1
	REACTOME: HLA-DQA1
	Pathway Commons: HLA-DQA1
Context	iHOP: HLA-DQA1
	ligand binding site mutation search in PubMed: HLA-DQA1
	UCL Cancer Institute: HLA-DQA1
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 HLA-DQA1

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
H50	E51K	SKCM	2
F83,F79	D81G	STAD	1
H50	F52C	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 HLA-DQA1

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
H50	F52C	-1.9296654
H50	E51K	-0.71837709

(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 HLA-DQA1 from PDB

PDB ID	PDB title	PDB structure
4GG6	Protein complex

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Differential gene expression and gene-gene network for HLA-DQA1

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 HLA-DQA1 and the right PPI network was created from samples without mutations in the LBS of HLA-DQA1. 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 HLA-DQA1

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0007570	Celiac Disease	70	Biomarker, GeneticVariation
umls:C0024141	Lupus Erythematosus, Systemic	13	Biomarker, GeneticVariation
umls:C0004096	Asthma	7	Biomarker, GeneticVariation
umls:C0020517	Hypersensitivity	3	Biomarker, GeneticVariation
umls:C0017665	Glomerulonephritis, Membranous	3	Biomarker, GeneticVariation
umls:C0011603	Dermatitis	2	Biomarker, GeneticVariation
umls:C0085179	Eosinophilia-Myalgia Syndrome	1	Biomarker, GeneticVariation
umls:C0014848	Esophageal Achalasia	1	Biomarker
umls:C0023290	Leishmaniasis, Visceral	1	Biomarker
umls:C0030305	Pancreatitis	1	Biomarker
umls:C0033687	Proteinuria	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for HLA-DQA1

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.