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 DMD

Gene summary

Basic gene Info.	Gene symbol	DMD
	Gene name	dystrophin
	Synonyms	BMD\|CMD3B\|DXS142\|DXS164\|DXS206\|DXS230\|DXS239\|DXS268\|DXS269\|DXS270\|DXS272\|MRX85
	Cytomap	UCSC genome browser: Xp21.2
	Type of gene	protein-coding
	RefGenes	NM_000109.3, NM_004006.2,NM_004009.3,NM_004010.3,NM_004011.3, NM_004012.3,NM_004013.2,NM_004014.2,NM_004015.2, NM_004016.2,NM_004017.2,NM_004018.2,NM_004019.2, NM_004020.3,NM_004021.2,NM_004022.2,NM_004023.2, NM_004007.2,
	Description	-
	Modification date	20141219
dbXrefs	MIM : 300377
	HGNC : HGNC
	Ensembl : ENSG00000198947
	HPRD : 02303
	Vega : OTTHUMG00000021336
Protein	UniProt: P11532 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DMD
	BioGPS: 1756
Pathway	NCI Pathway Interaction Database: DMD
	KEGG: DMD
	REACTOME: DMD
	Pathway Commons: DMD
Context	iHOP: DMD
	ligand binding site mutation search in PubMed: DMD
	UCL Cancer Institute: DMD
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:0043043	peptide biosynthetic process	16000376

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Ligand binding site mutations for DMD

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
T3188	R3187H	COAD	2
Q3079	P3078H	LUAD	1
Y3072	T3072K	LUAD	1
T3188	R3187P	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.

Clinical information for DMD from My Cancer Genome.

Dystrophin (DMD) is a gene that encodes a protein that functions in extracellular matrix degradation and non-integrin membrane-extracellular matrix interaction pathways. Missense mutations, silent mutations, nonsense mutations, and frameshift deletions are observed in cancers such as colon cancer, endometrial cancer, and skin cancer. Modified: August 27, 2015

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Protein structure related information for DMD

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

(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 DMD from PDB

PDB ID	PDB title	PDB structure
1DXX	N-TERMINAL ACTIN-BINDING DOMAIN OF HUMAN DYSTROPHIN

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Differential gene expression and gene-gene network for DMD

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0013264	Muscular Dystrophy, Duchenne	510	AlteredExpression, Biomarker, GeneticVariation
umls:C0026850	Muscular Dystrophies	451	AlteredExpression, Biomarker, GeneticVariation, Therapeutic
umls:C0917713	Becker muscular dystrophy	198	Biomarker, GeneticVariation
umls:C0007193	Cardiomyopathy, Dilated	40	AlteredExpression, Biomarker, GeneticVariation
umls:C0878544	Cardiomyopathies	35	Biomarker, GeneticVariation, Therapeutic
umls:C3714570	Dilated cardiomyopathy 3B	33	AlteredExpression, Biomarker, GeneticVariation
umls:C0206656	Rhabdomyosarcoma, Embryonal	2	Biomarker
umls:C0038220	Status Epilepticus	1	Biomarker
umls:C0238198	Gastrointestinal Stromal Tumors	1	Biomarker
umls:C0006663	Calcinosis	1	Biomarker
umls:C0018800	Cardiomegaly	1	Biomarker
umls:C0012644	Disease Models, Animal	1	Biomarker
umls:C0023269	Leiomyosarcoma	1	Biomarker
umls:C0026851	Muscular Dystrophy, Animal	1	Biomarker
umls:C0027540	Necrosis	1	Biomarker
umls:C0027626	Neoplasm Invasiveness	1	Biomarker
umls:C0027627	Neoplasm Metastasis	1	Biomarker
umls:C0032460	Polycystic Ovary Syndrome	1	Biomarker
umls:C0242973	Ventricular Dysfunction	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for DMD

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 DMD go to BioLip

Ligand ID

Ligand short name

Ligand long name

PDB ID

PDB name

mutLBS

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Conservation information for LBS of DMD

Multiple alignments for P11532 in multiple species

LBS	AA sequence	# species	Species
G3189	NVYDTGRTGRI	3	Homo sapiens, Mus musculus, Canis lupus familiaris
H3076	PYYINHETQTT	3	Homo sapiens, Mus musculus, Canis lupus familiaris
I3074	KVPYYINHETQ	3	Homo sapiens, Mus musculus, Canis lupus familiaris
N3068	RAISPNKVPYY	3	Homo sapiens, Mus musculus, Canis lupus familiaris
Q3079	INHETQTTCWD	3	Homo sapiens, Mus musculus, Canis lupus familiaris
R3190	VYDTGRTGRIR	3	Homo sapiens, Mus musculus, Canis lupus familiaris
S3066	WERAISPNKVP	3	Homo sapiens, Mus musculus, Canis lupus familiaris
T3081	HETQTTCWDHP	3	Homo sapiens, Mus musculus, Canis lupus familiaris
T3188	LNVYDTGRTGR	3	Homo sapiens, Mus musculus, Canis lupus familiaris
W3083	TQTTCWDHPKM	3	Homo sapiens, Mus musculus, Canis lupus familiaris
Y3072	PNKVPYYINHE	3	Homo sapiens, Mus musculus, Canis lupus familiaris