mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 LDHB
Gene summary
Basic gene Info.Gene symbolLDHB
Gene namelactate dehydrogenase B
SynonymsHEL-S-281|LDH-B|LDH-H|LDHBD|TRG-5
CytomapUCSC genome browser: 12p12.2-p12.1
Type of geneprotein-coding
RefGenesNM_001174097.1,
NM_002300.6,
DescriptionL-lactate dehydrogenase B chainLDH heart subunitepididymis secretory protein Li 281lactate dehydrogenase H chainrenal carcinoma antigen NY-REN-46
Modification date20141222
dbXrefs MIM : 150100
HGNC : HGNC
Ensembl : ENSG00000111716
HPRD : 01026
Vega : OTTHUMG00000133760
ProteinUniProt: P07195
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LDHB
BioGPS: 3945
PathwayNCI Pathway Interaction Database: LDHB
KEGG: LDHB
REACTOME: LDHB
Pathway Commons: LDHB
ContextiHOP: LDHB
ligand binding site mutation search in PubMed: LDHB
UCL Cancer Institute: LDHB
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


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Ligand binding site mutations for LDHB
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
LBSAAchange of nsSNVCancer type# samples
R100R100CCOAD1
R170,L166S168YCOAD1
R107R107PLUSC1
I253I253VLUSC1
Y84S85FSKCM1
V29V27LSTAD1
I253A252TUCEC1
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 LDHB
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.
LBSAAchange of nsSNVRelative stability change
R100R100C0.21680926
I253A252T-1.1244348
Y84S85F-0.74956074
I253I253V-0.7474699
R107R107P-0.45268087
L166S168Y-0.30577461
R170S168Y-0.30577461
V29V27L-0.17596945
(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 LDHB from PDB

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Differential gene expression and gene-gene network for LDHB
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 LDHB and the right PPI network was created from samples without mutations in the LBS of LDHB. 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 LDHB
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0007124Carcinoma, Intraductal, Noninfiltrating1Biomarker
umls:C0948089Acute Coronary Syndrome1Biomarker
umls:C1458155Breast Neoplasms1Biomarker
umls:C0007134Carcinoma, Renal Cell1Biomarker
umls:C0025521Metabolism, Inborn Errors1Biomarker
umls:C0027626Neoplasm Invasiveness1Biomarker
umls:C0033578Prostatic Neoplasms1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for LDHB
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 statusDrugBank IDNameTypeDrug structure
NutraceuticalDB00157NADHSmall molecule
ExperimentalDB024014-Hydroxy-1,2,5-Oxadiazole-3-Carboxylic AcidSmall molecule
ExperimentalDB03940Oxamic AcidSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of LDHB go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of LDHB
Multiple alignments for P07195 in multiple species
LBSAA sequence# speciesSpecies
A239MVVDSAYEVIK3Danio rerio, Mus musculus, Rattus norvegicus
A239MVVESAYEVIK2Homo sapiens, Pan troglodytes
A239KVVDSAYEVIR1Danio rerio
A239QVVESAYEVIR1Gallus gallus
A97IVVVTAGVRQQ7Homo sapiens, Danio rerio, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
D53ELALVDVLEDK5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
D53ELALVDVVEDK1Danio rerio
D53ELALVDVVEDR1Danio rerio
G30TVVGVGQVGMA6Homo sapiens, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
G30TIVGVGQVGMA1Danio rerio
G98VVVTAGVRQQE7Homo sapiens, Danio rerio, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
H194WILGEHGDSSV6Homo sapiens, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
H194YILGEHGDTSV1Danio rerio
I121NVFKFIIPQIV5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
I121NIFKHIIPQIV2Danio rerio, Danio rerio
I253YTNWAIGLSVA7Homo sapiens, Danio rerio, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
L166GSGCNLDSARF4Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus
L166GSGTNLDSARF2Danio rerio, Danio rerio
L166GSGCNLDTARF1Gallus gallus
L55ALVDVLEDKLK5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
L55ALVDVVEDKLK1Danio rerio
L55ALVDVVEDRLK1Danio rerio
N139IIVVSNPVDIL4Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus
N139LIVVSNPVDVL1Danio rerio
N139LVVVSNPVDVL1Danio rerio
N139ILVVSNPVDIL1Gallus gallus
Q101TAGVRQQEGES7Homo sapiens, Danio rerio, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
Q31VVGVGQVGMAC6Homo sapiens, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
Q31IVGVGQVGMAC1Danio rerio
R100VTAGVRQQEGE7Homo sapiens, Danio rerio, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
R107QEGESRLNLVQ7Homo sapiens, Danio rerio, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
R170NLDSARFRYLM5Homo sapiens, Danio rerio, Pan troglodytes, Mus musculus, Rattus norvegicus
R170NLDSARFRYIM1Danio rerio
R170NLDTARFRYLM1Gallus gallus
S138IIIVVSNPVDI2Homo sapiens, Pan troglodytes
S138TIIVVSNPVDI2Mus musculus, Rattus norvegicus
S138ILIVVSNPVDV1Danio rerio
S138ILVVVSNPVDV1Danio rerio
S138TILVVSNPVDI1Gallus gallus
S162HRVIGSGCNLD5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
S162HRVIGSGTNLD2Danio rerio, Danio rerio
T249KLKGYTNWAIG5Homo sapiens, Danio rerio, Pan troglodytes, Mus musculus, Rattus norvegicus
T249RLKGYTNWAIG2Danio rerio, Gallus gallus
T96KIVVVTAGVRQ5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
T96RIVVVTAGVRQ2Danio rerio, Danio rerio
V117QRNVNVFKFII5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
V117QRNVNIFKHII2Danio rerio, Danio rerio
V137CIIIVVSNPVD2Homo sapiens, Pan troglodytes
V137CTIIVVSNPVD2Mus musculus, Rattus norvegicus
V137CILIVVSNPVD1Danio rerio
V137CILVVVSNPVD1Danio rerio
V137CTILVVSNPVD1Gallus gallus
V141VVSNPVDILTY5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
V141VVSNPVDVLTY2Danio rerio, Danio rerio
V29ITVVGVGQVGM5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
V29VTVVGVGQVGM1Danio rerio
V29VTIVGVGQVGM1Danio rerio
V32VGVGQVGMACA7Homo sapiens, Danio rerio, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
V54LALVDVLEDKL5Homo sapiens, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
V54LALVDVVEDKL1Danio rerio
V54LALVDVVEDRL1Danio rerio
V99VVTAGVRQQEG7Homo sapiens, Danio rerio, Danio rerio, Gallus gallus, Pan troglodytes, Mus musculus, Rattus norvegicus
Y84VADKDYSVTAN5Homo sapiens, Danio rerio, Pan troglodytes, Mus musculus, Rattus norvegicus
Y84VSGKDYSVTAN1Danio rerio
Y84VADKDYAVTAN1Gallus gallus


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