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 LCN2
Gene summary
Basic gene Info.Gene symbolLCN2
Gene namelipocalin 2
Synonyms24p3|MSFI|NGAL
CytomapUCSC genome browser: 9q34
Type of geneprotein-coding
RefGenesNM_005564.3,
Description25 kDa alpha-2-microglobulin-related subunit of MMP-9lipocalin-2migration-stimulating factor inhibitorneutrophil gelatinase-associated lipocalinoncogene 24p3p25siderocalin LCN2
Modification date20141207
dbXrefs MIM : 600181
HGNC : HGNC
Ensembl : ENSG00000148346
HPRD : 02551
Vega : OTTHUMG00000020734
ProteinUniProt: P80188
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LCN2
BioGPS: 3934
PathwayNCI Pathway Interaction Database: LCN2
KEGG: LCN2
REACTOME: LCN2
Pathway Commons: LCN2
ContextiHOP: LCN2
ligand binding site mutation search in PubMed: LCN2
UCL Cancer Institute: LCN2
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 LCN2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
F153F153LBLCA1
K154K154QHNSC1
T156,Y158L157IUCEC1
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 LCN2
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
T156L157I-1.5219365
Y158L157I-1.5219365
K154K154Q-0.68939564
F153F153L-0.60242712
(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 LCN2 from PDB

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Differential gene expression and gene-gene network for LCN2
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 LCN2 and the right PPI network was created from samples without mutations in the LBS of LCN2. 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 LCN2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0027627Neoplasm Metastasis16Biomarker, GeneticVariation
umls:C0022658Kidney Diseases9AlteredExpression, Biomarker
umls:C0027651Neoplasms6Biomarker, Therapeutic
umls:C2609414Acute Kidney Injury4Biomarker
umls:C0005283beta-Thalassemia2AlteredExpression, Biomarker
umls:C0021368Inflammation2Biomarker
umls:C0860207Drug-Induced Liver Injury2Biomarker
umls:C0003873Arthritis, Rheumatoid1Biomarker
umls:C0006663Calcinosis1Biomarker
umls:C0018824Heart Valve Diseases1Biomarker
umls:C0019188Hepatitis, Animal1Biomarker
umls:C0023893Liver Cirrhosis, Experimental1Biomarker

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

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Pharmacological information for LCN2
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
ExperimentalDB01631Methyl Nonanoate (Ester)Small molecule
ExperimentalDB016722,3-Dihydroxy-Benzoic AcidSmall molecule
ExperimentalDB01926Carboxymycobactin SSmall molecule
ExperimentalDB027102,3,-DihydroxybenzoylserineSmall molecule
ExperimentalDB04043Carboxymycobactin TSmall molecule
ExperimentalDB04476Trencam-3,2-HopoSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of LCN2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of LCN2
Multiple alignments for P80188 in multiple species
LBSAA sequence# speciesSpecies
A60GLAGNAILRED1Homo sapiens
A60GLAGNAVQKKT1Mus musculus
A60GLAGNAVQKER1Rattus norvegicus
D81YELKEDKSYNV1Homo sapiens
D81YELQENNSYNV1Mus musculus
D81YELQEDNSYNV1Rattus norvegicus
E64NAILREDKDPQ1Homo sapiens
E64NAVQKKTEGSF1Mus musculus
E64NAVQKERQSRF1Rattus norvegicus
F143HAMVFFKKVSQ1Homo sapiens
F143FAMVFFRKTSE1Mus musculus
F143FAMVFFQKTSE1Rattus norvegicus
F153QNREYFKITLY1Homo sapiens
F153ENKQYFKITLY1Mus musculus
F153ENKQYFKVTLY1Rattus norvegicus
I61LAGNAILREDK1Homo sapiens
I61LAGNAVQKKTE1Mus musculus
I61LAGNAVQKERQ1Rattus norvegicus
K145MVFFKKVSQNR1Homo sapiens
K145MVFFRKTSENK1Mus musculus
K145MVFFQKTSENK1Rattus norvegicus
K154NREYFKITLYG1Homo sapiens
K154NKQYFKITLYG1Mus musculus
K154NKQYFKVTLYG1Rattus norvegicus
K70DKDPQKMYATI1Homo sapiens
K70TEGSFTMYSTI1Mus musculus
K70RQSRFTMYSTI1Rattus norvegicus
L114PGEFTLGNIKS1Homo sapiens
L114AGQFTLGNMHR1Mus musculus
L114PGQFTLGNIHS1Rattus norvegicus
L123KSYPGLTSYLV1Homo sapiens
L123HRYPQVQSYNV1Mus musculus
L123HSYPQIQSYDV1Rattus norvegicus
L56WYVVGLAGNAI1Homo sapiens
L56WYVVGLAGNAV1Mus musculus
L56WFVVGLAGNAV1Rattus norvegicus
L62AGNAILREDKD1Homo sapiens
L62AGNAVQKKTEG1Mus musculus
L62AGNAVQKERQS1Rattus norvegicus
L90NVTSVLFR--K1Homo sapiens
L90NVTSILVRDQD1Mus musculus
L90NVTSILVR--G1Rattus norvegicus
N136VSTNYNQHAMV1Homo sapiens
N136ATTDYNQFAMV1Mus musculus
N136ADTDYDQFAMV1Rattus norvegicus
P189NHIVFPVPIDQ1Homo sapiens
P189DNIIFSVPTDQ1Mus musculus
P189NNIVFSVPTDQ1Rattus norvegicus
Q43LQQNFQDNQFQ1Homo sapiens
Q43LQPDFRSDQFR1Mus musculus
Q43LQPGFWTERFQ1Rattus norvegicus
Q46NFQDNQFQGKW1Homo sapiens
Q46DFRSDQFRGRW1Mus musculus
Q46GFWTERFQGRW1Rattus norvegicus
Q69EDKDPQKMYAT1Homo sapiens
Q69KTEGSFTMYST1Mus musculus
Q69ERQSRFTMYST1Rattus norvegicus
R101CRYWIRTFVPS2Mus musculus, Rattus norvegicus
R101CDYWIRTFVPG1Homo sapiens
R160ITLYGRTKELT1Homo sapiens
R160ITLYGRTKELS1Mus musculus
R160VTLYGRTKGLS1Rattus norvegicus
R63GNAILREDKDP1Homo sapiens
R63GNAVQKKTEGS1Mus musculus
R63GNAVQKERQSR1Rattus norvegicus
R92TSVLFR--KKK1Homo sapiens
R92TSILVRDQDQG1Mus musculus
R92TSILVR--GQG1Rattus norvegicus
S147FFKKVSQNREY1Homo sapiens
S147FFRKTSENKQY1Mus musculus
S147FFQKTSENKQY1Rattus norvegicus
S83LKEDKSYNVTS1Homo sapiens
S83LQENNSYNVTS1Mus musculus
S83LQEDNSYNVTS1Rattus norvegicus
S88SYNVTSVLFR-1Homo sapiens
S88SYNVTSILVRD1Mus musculus
S88SYNVTSILVR-1Rattus norvegicus
T102RYWIRTFVPSS2Mus musculus, Rattus norvegicus
T102DYWIRTFVPGC1Homo sapiens
T156EYFKITLYGRT1Homo sapiens
T156QYFKITLYGRT1Mus musculus
T156QYFKVTLYGRT1Rattus norvegicus
T74FTMYSTIYELQ2Mus musculus, Rattus norvegicus
T74QKMYATIYELK1Homo sapiens
V104WIRTFVPGCQP1Homo sapiens
V104WIRTFVPSSRA1Mus musculus
V104WIRTFVPSSRP1Rattus norvegicus
V86DKSYNVTSVLF1Homo sapiens
V86NNSYNVTSILV1Mus musculus
V86DNSYNVTSILV1Rattus norvegicus
W99QGCRYWIRTFV2Mus musculus, Rattus norvegicus
W99KKCDYWIRTFV1Homo sapiens
Y120GNIKSYPGLTS1Homo sapiens
Y120GNMHRYPQVQS1Mus musculus
Y120GNIHSYPQIQS1Rattus norvegicus
Y126PGLTSYLVRVV1Homo sapiens
Y126PQVQSYNVQVA1Mus musculus
Y126PQIQSYDVQVA1Rattus norvegicus
Y135VVSTNYNQHAM1Homo sapiens
Y135VATTDYNQFAM1Mus musculus
Y135VADTDYDQFAM1Rattus norvegicus
Y152SQNREYFKITL1Homo sapiens
Y152SENKQYFKITL1Mus musculus
Y152SENKQYFKVTL1Rattus norvegicus
Y158FKITLYGRTKE2Homo sapiens, Mus musculus
Y158FKVTLYGRTKG1Rattus norvegicus
Y72DPQKMYATIYE1Homo sapiens
Y72GSFTMYSTIYE1Mus musculus
Y72SRFTMYSTIYE1Rattus norvegicus


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