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 NEDD4

Gene summary

Basic gene Info.	Gene symbol	NEDD4
	Gene name	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase
	Synonyms	NEDD4-1\|RPF1
	Cytomap	UCSC genome browser: 15q
	Type of gene	protein-coding
	RefGenes	NM_001284338.1, NM_001284339.1,NM_001284340.1,NM_006154.3,NM_198400.3, NR_104302.1,
	Description	E3 ubiquitin-protein ligase NEDD4cell proliferation-inducing gene 53 proteinneural precursor cell expressed developmentally down-regulated protein 4receptor-potentiating factor 1
	Modification date	20141207
dbXrefs	MIM : 602278
	HGNC : HGNC
	Ensembl : ENSG00000069869
	HPRD : 03786
	Vega : OTTHUMG00000132015
Protein	UniProt: P46934 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NEDD4
	BioGPS: 4734
Pathway	NCI Pathway Interaction Database: NEDD4
	KEGG: NEDD4
	REACTOME: NEDD4
	Pathway Commons: NEDD4
Context	iHOP: NEDD4
	ligand binding site mutation search in PubMed: NEDD4
	UCL Cancer Institute: NEDD4
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:0006622	protein targeting to lysosome	17116753
GO:0007041	lysosomal transport	18544533
GO:0010766	negative regulation of sodium ion transport	10642508
GO:0016567	protein ubiquitination	18305167
GO:0031623	receptor internalization	18544533
GO:0032801	receptor catabolic process	18544533
GO:0034765	regulation of ion transmembrane transport	17289006
GO:0042391	regulation of membrane potential	17289006
GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	20086093
GO:0042921	glucocorticoid receptor signaling pathway	8649367
GO:0045732	positive regulation of protein catabolic process	14973438
GO:0046824	positive regulation of nucleocytoplasmic transport	17218261
GO:0050847	progesterone receptor signaling pathway	8649367
GO:1901016	regulation of potassium ion transmembrane transporter activity	17289006

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Ligand binding site mutations for NEDD4

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
N853	G854W	LUAD	1
S1218	Y1217C	LUAD	1
W868	W868S	SKCM	1
N1047	E1048K	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 NEDD4

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
S1218	Y1217C	-1.2318339
W868	W868S	-0.96480986
N1047	E1048K	-0.94038071
N853	G854W	-0.23227293

(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 NEDD4 from PDB

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Differential gene expression and gene-gene network for NEDD4

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 NEDD4 and the right PPI network was created from samples without mutations in the LBS of NEDD4. 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 NEDD4

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0022548	Keloid	3	Biomarker, GeneticVariation
umls:C0151744	Myocardial Ischemia	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for NEDD4

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.