mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

	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 NFKB2

Gene summary

Basic gene Info.	Gene symbol	NFKB2
	Gene name	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)
	Synonyms	CVID10\|H2TF1\|LYT-10\|LYT10\|NF-kB2\|p100\|p52
	Cytomap	UCSC genome browser: 10q24
	Type of gene	protein-coding
	RefGenes	NM_001077494.3, NM_001261403.2,NM_001288724.1,NM_002502.5,
	Description	DNA-binding factor KBF2NFKB, p52/p100 subunitlymphocyte translocation chromosome 10 proteinnuclear factor Kappa-B, subunit 2nuclear factor NF-kappa-B p100 subunitnuclear factor NF-kappa-B p52 subunitnuclear factor of Kappa light chain gene enhancer
	Modification date	20141207
dbXrefs	MIM : 164012
	HGNC : HGNC
	Ensembl : ENSG00000077150
	HPRD : 01239
	Vega : OTTHUMG00000018962
Protein	UniProt: Q00653 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NFKB2
	BioGPS: 4791
Pathway	NCI Pathway Interaction Database: NFKB2
	KEGG: NFKB2
	REACTOME: NFKB2
	Pathway Commons: NFKB2
Context	iHOP: NFKB2
	ligand binding site mutation search in PubMed: NFKB2
	UCL Cancer Institute: NFKB2
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:0006355	regulation of transcription, DNA-templated	8360178
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	12835724

Top

Ligand binding site mutations for NFKB2

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
H62	G64R	BLCA	1
R52	R52Q	COAD	1
P223	G224E	LUAD	1
K144	M146V	STAD	1
R54	R54Q	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.

Top

Protein structure related information for NFKB2

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
R54	R54Q	-1.689946
K144	M146V	-1.480263
H62	G64R	-0.67655068
R52	R52Q	-0.62766798
P223	G224E	-0.20715952

(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 NFKB2 from PDB

Top

Differential gene expression and gene-gene network for NFKB2

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 NFKB2 and the right PPI network was created from samples without mutations in the LBS of NFKB2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

Top

Phenotype information for NFKB2

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0018843	Heat Stroke	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

Top

Pharmacological information for NFKB2

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\|vet_approved	DB00945	Acetylsalicylic acid	Small molecule
Approved	DB01296	Glucosamine	Small molecule
Investigational	DB05212	HE3286	Small molecule
Investigational	DB05451	P54	Small molecule
Investigational	DB05464	NOX-700	Small molecule
Investigational	DB05471	SGN-30	Biotech
Investigational	DB05487	CC-8490	Small molecule
Investigational	DB05767	HMPL-004	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NFKB2 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
NUC		Nucleic Acids	1a3q	A	R52 H62 P223
NUC		Nucleic Acids	1a3q	B	R52 P223
NUC		Nucleic Acids	3do7	B	R52 P223
NUC		Nucleic Acids	1a3q	A	R52 R54 H62
NUC		Nucleic Acids	3do7	B	R52 R54 H62
NUC		Nucleic Acids	1a3q	B	R52 R54 K144

Top

Conservation information for LBS of NFKB2

Multiple alignments for Q00653 in multiple species

LBS

AA sequence

# species

Species