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 NEU2

Gene summary

Basic gene Info.	Gene symbol	NEU2
	Gene name	sialidase 2 (cytosolic sialidase)
	Synonyms	SIAL2
	Cytomap	UCSC genome browser: 2q37
	Type of gene	protein-coding
	RefGenes	NM_005383.2,
	Description	N-acetyl-alpha-neuraminidase 2cytosolic sialidaseneuraminidase 2sialidase-2
	Modification date	20141207
dbXrefs	MIM : 605528
	HGNC : HGNC
	Ensembl : ENSG00000115488
	HPRD : 05702
	Vega : OTTHUMG00000133274
Protein	UniProt: Q9Y3R4 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NEU2
	BioGPS: 4759
Pathway	NCI Pathway Interaction Database: NEU2
	KEGG: NEU2
	REACTOME: NEU2
	Pathway Commons: NEU2
Context	iHOP: NEU2
	ligand binding site mutation search in PubMed: NEU2
	UCL Cancer Institute: NEU2
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:0006689	ganglioside catabolic process	22228546
GO:0009313	oligosaccharide catabolic process	22228546

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Ligand binding site mutations for NEU2

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
Y334	D336N	BLCA	1
Q270	Q270H	COAD	1
Y334	A333S	LUAD	1
N86	P87L	SKCM	1
Y179	A178T	STAD	1
R41	R41W	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 NEU2

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
Y334	A333S	-1.3434214
Y179	A178T	-1.2092484
Q270	Q270H	-0.70011493
Y334	D336N	-0.48277283
R41	R41W	-0.2527987
N86	P87L	-0.17855029

(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 NEU2 from PDB

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Differential gene expression and gene-gene network for NEU2

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 NEU2 and the right PPI network was created from samples without mutations in the LBS of NEU2. 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 NEU2

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for NEU2

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.

Gene-centered drug-gene interaction network

Drug information targeting mutLBSgene (Approved drugs only)

Drug status	DrugBank ID	Name	Type	Drug structure
Approved	DB00198	Oseltamivir	Small molecule
Approved\|investigational	DB00558	Zanamivir	Small molecule
Experimental	DB03991	2-Deoxy-2,3-Dehydro-N-Acetyl-Neuraminic Acid	Small molecule
Experimental	DB07960	5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-6-ISOBUTOXY-4H-PYRAN-2-CARBOXYLIC ACID	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NEU2 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
ZMR		ZANAMIVIR	2f0z	A	N86 Y179 Y334
DAN		DANA	2f25	A	N86 Y179 Y334
DAN		DANA	2f27	B	N86 Y179 Y334
DAN		DANA	2f29	B	N86 Y179 Y334
DAN		DANA	1vcu	B	N86 Y334
IEM		ISOBUTYL ETHER MIMETIC	2f11	A	R41 N86 Q270 Y334
DAN		DANA	2f25	B	R41 N86 Y179 Q270 Y334
DAN		DANA	1vcu	A	R41 N86 Y179 Y334
BCZ		PERAMIVIR	2f10	A	R41 N86 Y179 Y334
DAN		DANA	2f27	A	R41 N86 Y179 Y334
FSI		3-FLUOROSIALIC ACID	4nc5	A	R41 N86 Y179 Y334
DYM		2,3-DIHYDROXYPROPYL ETHER MIMETIC	2f13	A	R41 N86 Y334
FSR	2,3-DIFLUOROSIALIC ACID	(2S,3S,4R,5R,6R)-5-ACETAMIDO-2,3-BIS(FLUORANYL)-4- OXIDANYL-6-[(1S,2S)-1,2,3-TRIS(OXIDANYL)PROPYL]OXANE- 2-CARBOXYLIC ACID	4ncs	A	R41 Y179 Y334
DAN		DANA	2f29	A	Y179 Y334
HTM		3-HYDROXYPROPYL ETHER MIMETIC	2f12	A	Y334

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Conservation information for LBS of NEU2

Multiple alignments for Q9Y3R4 in multiple species

LBS

AA sequence

# species

Species