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-DRA

Gene summary

Basic gene Info.	Gene symbol	HLA-DRA
	Gene name	major histocompatibility complex, class II, DR alpha
	Synonyms	HLA-DRA1\|MLRW
	Cytomap	UCSC genome browser: 6p21.3
	Type of gene	protein-coding
	RefGenes	NM_019111.4,
	Description	HLA class II histocompatibility antigen, DR alpha chainMHC cell surface glycoproteinMHC class II antigen DRAhistocompatibility antigen HLA-DR alpha
	Modification date	20141207
dbXrefs	MIM : 142860
	HGNC : HGNC
	Ensembl : ENSG00000204287
	HPRD : 00833
	Vega : OTTHUMG00000031269
Protein	UniProt: P01903 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HLA-DRA
	BioGPS: 3122
Pathway	NCI Pathway Interaction Database: HLA-DRA
	KEGG: HLA-DRA
	REACTOME: HLA-DRA
	Pathway Commons: HLA-DRA
Context	iHOP: HLA-DRA
	ligand binding site mutation search in PubMed: HLA-DRA
	UCL Cancer Institute: HLA-DRA
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:0002503	peptide antigen assembly with MHC class II protein complex	1448172
GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	21502329
GO:0002506	polysaccharide assembly with MHC class II protein complex	21502329

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Ligand binding site mutations for HLA-DRA

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
F57	V59A	COAD	1
W68	R69W	COAD	1
M98	M98T	COAD	1
Y104	P106L	GBM	1
W68	V67I	LUAD	1
M98	M98I	OV	1
R75	R75Q	SKCM	1
R101	R101H	STAD	1
R101	R101C	STAD	1
Y104	P106L	STAD	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-DRA

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
M98	M98T	-1.3843026
R75	R75Q	-1.2108618
R101	R101H	-1.1772802
M98	M98I	-0.92872042
R101	R101C	-0.90807345
F57	V59A	-0.84250241
W68	R69W	-0.81844931
Y104	P106L	-0.51798197
W68	V67I	-0.46239908

(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-DRA from PDB

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

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0026769	Multiple Sclerosis	9	Biomarker, GeneticVariation
umls:C0030567	Parkinson Disease	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 HLA-DRA

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.