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 NRXN1

Gene summary

Basic gene Info.	Gene symbol	NRXN1
	Gene name	neurexin 1
	Synonyms	Hs.22998\|PTHSL2\|SCZD17
	Cytomap	UCSC genome browser: 2p16.3
	Type of gene	protein-coding
	RefGenes	NM_001135659.1, NM_004801.4,NM_138735.2,
	Description	neurexin Ineurexin-1-beta
	Modification date	20141222
dbXrefs	MIM : 600565
	HGNC : HGNC
	Ensembl : ENSG00000179915
	HPRD : 11858
	Vega : OTTHUMG00000129263
Protein	UniProt: Q9ULB1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NRXN1
	BioGPS: 9378
Pathway	NCI Pathway Interaction Database: NRXN1
	KEGG: NRXN1
	REACTOME: NRXN1
	Pathway Commons: NRXN1
Context	iHOP: NRXN1
	ligand binding site mutation search in PubMed: NRXN1
	UCL Cancer Institute: NRXN1
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 NRXN1

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
V158	V158F	LUAD	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 NRXN1

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 NRXN1 from PDB

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Differential gene expression and gene-gene network for NRXN1

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 NRXN1 and the right PPI network was created from samples without mutations in the LBS of NRXN1. 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 NRXN1

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0036341	Schizophrenia	34	Biomarker, GeneticVariation
umls:C0004352	Autistic Disorder	21	Biomarker, GeneticVariation
umls:C3714756	Intellectual Disability	5	Biomarker
umls:C1970431	Pitt-Hopkins syndrome	4	Biomarker
umls:C0023014	Language Development Disorders	3	Biomarker, GeneticVariation
umls:C0000772	Abnormalities, Multiple	1	Biomarker
umls:C0008074	Child Development Disorders, Pervasive	1	Biomarker
umls:C0376634	Craniofacial Abnormalities	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for NRXN1

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.