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 TNFSF13B

Gene summary

Basic gene Info.	Gene symbol	TNFSF13B
	Gene name	tumor necrosis factor (ligand) superfamily, member 13b
	Synonyms	BAFF\|BLYS\|CD257\|DTL\|TALL-1\|TALL1\|THANK\|TNFSF20\|ZTNF4
	Cytomap	UCSC genome browser: 13q32-q34
	Type of gene	protein-coding
	RefGenes	NM_001145645.2, NM_006573.4,
	Description	ApoL related ligand TALL-1B-cell-activating factorB-lymphocyte stimulatorDelta4 BAFFTNF and ApoL-related leukocyte expressed ligand 1TNF homolog that activates apoptosisdelta BAFFdendritic cell-derived TNF-like moleculetumor necrosis factor (ligan
	Modification date	20141222
dbXrefs	MIM : 603969
	HGNC : HGNC
	Ensembl : ENSG00000102524
	HPRD : 04914
	Vega : OTTHUMG00000017329
Protein	UniProt: Q9Y275 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TNFSF13B
	BioGPS: 10673
Pathway	NCI Pathway Interaction Database: TNFSF13B
	KEGG: TNFSF13B
	REACTOME: TNFSF13B
	Pathway Commons: TNFSF13B
Context	iHOP: TNFSF13B
	ligand binding site mutation search in PubMed: TNFSF13B
	UCL Cancer Institute: TNFSF13B
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 TNFSF13B

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
D275	D273N	STAD	1
R231	R231Q	UCEC	1
L211	I212L	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 TNFSF13B

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
R231	R231Q	-1.1963695
D275	D273N	-0.62194653
L211	I212L	-0.46115706

(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 TNFSF13B from PDB

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Differential gene expression and gene-gene network for TNFSF13B

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 TNFSF13B and the right PPI network was created from samples without mutations in the LBS of TNFSF13B. 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 TNFSF13B

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 TNFSF13B

Gene-centered drug-gene interaction network

Drug information targeting mutLBSgene (Approved drugs only)

Drug status	DrugBank ID	Name	Type	Drug structure
Experimental	DB03316	1,4-Diethylene Dioxide	Small molecule
Nutraceutical\|vet_approved	DB04272	Citric Acid	Small molecule
Approved	DB08879	Belimumab	Biotech

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of TNFSF13B go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	B	D275
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	D	D275
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	E	D275
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	F	D275
III		Peptide ligand (ACE,CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	B	D275
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	D	D275
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	F	D275
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	C	L211 R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	E	L211 R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	A	R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	B	R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	D	R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS)	1osg	F	R231
III		Peptide ligand (ACE,CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	A	R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	B	R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	C	R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	D	R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	E	R231
III		Peptide ligand (CYS,HIS,TRP,ASP,LEU,LEU,VAL,ARG,HIS,TRP,VAL,CYS,NH2)	3v56	F	R231

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Conservation information for LBS of TNFSF13B

Multiple alignments for Q9Y275 in multiple species

LBS

AA sequence

# species

Species