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 APOA1
Gene summary
Basic gene Info.Gene symbolAPOA1
Gene nameapolipoprotein A-I
Synonyms-
CytomapUCSC genome browser: 11q23-q24
Type of geneprotein-coding
RefGenesNM_000039.1,
Descriptionapo-AI
Modification date20141222
dbXrefs MIM : 107680
HGNC : HGNC
Ensembl : ENSG00000118137
HPRD : 02517
Vega : OTTHUMG00000046112
ProteinUniProt: P02647
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APOA1
BioGPS: 335
PathwayNCI Pathway Interaction Database: APOA1
KEGG: APOA1
REACTOME: APOA1
Pathway Commons: APOA1
ContextiHOP: APOA1
ligand binding site mutation search in PubMed: APOA1
UCL Cancer Institute: APOA1
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
GO:0002740negative regulation of cytokine secretion involved in immune response12458630
GO:0006656phosphatidylcholine biosynthetic process4335615
GO:0007179transforming growth factor beta receptor signaling pathway23726972
GO:0007186G-protein coupled receptor signaling pathway16443932
GO:0007229integrin-mediated signaling pathway23726972
GO:0010804negative regulation of tumor necrosis factor-mediated signaling pathway21571275
GO:0010873positive regulation of cholesterol esterification4335615
GO:0010903negative regulation of very-low-density lipoprotein particle remodeling14967812
GO:0018158protein oxidation12576517
GO:0018206peptidyl-methionine modification12576517
GO:0030301cholesterol transport10559507
GO:0032489regulation of Cdc42 protein signal transduction16443932
GO:0033344cholesterol efflux11162594
GO:0033700phospholipid efflux11162594
GO:0034115negative regulation of heterotypic cell-cell adhesion21571275
GO:0034380high-density lipoprotein particle assembly190223
GO:0035025positive regulation of Rho protein signal transduction23726972
GO:0042632cholesterol homeostasis21571275
GO:0050713negative regulation of interleukin-1 beta secretion12458630
GO:0050728negative regulation of inflammatory response21571275
GO:0050821protein stabilization17655203
GO:0050919negative chemotaxis23726972
GO:0051345positive regulation of hydrolase activity7638166
GO:0051496positive regulation of stress fiber assembly23726972
GO:0055091phospholipid homeostasis21571275
GO:0060354negative regulation of cell adhesion molecule production21571275
GO:0060761negative regulation of response to cytokine stimulus21571275
GO:0070328triglyceride homeostasis21571275
GO:0070371ERK1 and ERK2 cascade23726972
GO:1900026positive regulation of substrate adhesion-dependent cell spreading23726972


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Ligand binding site mutations for APOA1
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
E259E258QLUAD1
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 APOA1
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
E259E258Q-0.40889893
(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 APOA1 from PDB

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Differential gene expression and gene-gene network for APOA1
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 APOA1 and the right PPI network was created from samples without mutations in the LBS of APOA1. 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 APOA1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C2239176Carcinoma, Hepatocellular16AlteredExpression, Biomarker
umls:C0039292Tangier Disease14Biomarker, GeneticVariation
umls:C0020538Hypertension7Biomarker, GeneticVariation
umls:C1704429Familial hypoalphalipoproteinemia7Biomarker, GeneticVariation
umls:C0038454Stroke5AlteredExpression, Biomarker, GeneticVariation
umls:C0019693HIV Infections4AlteredExpression, Biomarker
umls:C0268389Amyloidosis, familial visceral3Biomarker, GeneticVariation
umls:C0021368Inflammation3Biomarker, GeneticVariation, Therapeutic
umls:C0038356Stomach Neoplasms3Biomarker
umls:C0473527Hypoalphalipoproteinemias2Biomarker, GeneticVariation
umls:C0001418Adenocarcinoma2AlteredExpression, Biomarker
umls:C0024121Lung Neoplasms2AlteredExpression, Biomarker
umls:C0853897Diabetic Cardiomyopathies1Biomarker, Therapeutic
umls:C0242488Acute Lung Injury1Therapeutic
umls:C0152013Adenocarcinoma of lung1Biomarker
umls:C0003130Anoxia1Biomarker
umls:C1848533Ataxia with vitamin E deficiency1Biomarker
umls:C0004943Behcet Syndrome1Biomarker
umls:C0011065Death1Therapeutic
umls:C0011609Drug Eruptions1Biomarker
umls:C0860207Drug-Induced Liver Injury1Biomarker
umls:C0013604Edema1Therapeutic
umls:C0017665Glomerulonephritis, Membranous1Biomarker

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

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Pharmacological information for APOA1
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of APOA1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of APOA1
Multiple alignments for P02647 in multiple species
LBSAA sequence# speciesSpecies
A199LRQRLAARLEA3Homo sapiens, Pan troglodytes, Macaca mulatta
A199VRTKLTERLED1Danio rerio
A199LRQKLSQKLEE1Gallus gallus
A199LRQRLTARLEA1Bos taurus
A199MRENLAQRLTE1Rattus norvegicus
A199MRESLAQRLAE1Mus musculus
A200RQRLAARLEAL3Homo sapiens, Pan troglodytes, Macaca mulatta
A200RTKLTERLEDL1Danio rerio
A200RQKLSQKLEEI1Gallus gallus
A200RQRLTARLEAL1Bos taurus
A200RENLAQRLTEI1Rattus norvegicus
A200RESLAQRLAEL1Mus musculus
E222HAKATEHLSTL2Homo sapiens, Pan troglodytes
E222KEQLVKAVEEA1Danio rerio
E222QAKVMEQLSNL1Gallus gallus
E222HAKASEQLKAL1Bos taurus
E222HAKASEHLSTL1Macaca mulatta
E222HTKASDHLKTL1Rattus norvegicus
E222HTRAKTHLKTL1Mus musculus
E259LSALEEYTKKL3Homo sapiens, Pan troglodytes, Macaca mulatta
E259AQMYETIAKAI1Danio rerio
E259ISFLDELQKSV1Gallus gallus
E259LAAIDEASKKL1Bos taurus
E259MSMIDEAKKKL1Rattus norvegicus
E259QSVIDKASETL1Mus musculus
H217RLAEYHAKATE2Homo sapiens, Pan troglodytes
H217YAEEYKEQLVK1Danio rerio
H217QASEYQAKVME1Gallus gallus
H217-LAEYHAKASE1Bos taurus
H217RLAEYHAKASE1Macaca mulatta
H217TLIEYHTKASD1Rattus norvegicus
H217TLNEYHTRAKT1Mus musculus
H223AKATEHLSTLS2Homo sapiens, Pan troglodytes
H223EQLVKAVEEAR1Danio rerio
H223AKVMEQLSNLR1Gallus gallus
H223AKASEQLKALG1Bos taurus
H223AKASEHLSTLS1Macaca mulatta
H223TKASDHLKTLG1Rattus norvegicus
H223TRAKTHLKTLG1Mus musculus
K219AEYHAKATEHL2Homo sapiens, Pan troglodytes
K219EEYKEQLVKAV1Danio rerio
K219SEYQAKVMEQL1Gallus gallus
K219AEYHAKASEQL1Bos taurus
K219AEYHAKASEHL1Macaca mulatta
K219IEYHTKASDHL1Rattus norvegicus
K219NEYHTRAKTHL1Mus musculus
K230STLSEKAKPAL3Homo sapiens, Pan troglodytes, Macaca mulatta
K230EEAREKIAPHT1Danio rerio
K230SNLREKMTPLV1Gallus gallus
K230KALGEKAKPVL1Bos taurus
K230KTLGEKAKPAL1Rattus norvegicus
K230KTLGEKARPAL1Mus musculus
L242DLRQGLLPVLE4Homo sapiens, Bos taurus, Pan troglodytes, Macaca mulatta
L242DLQTRMEPYME1Danio rerio
L242EFRERLTPYAE1Gallus gallus
L242DLGQGLMPVLE1Rattus norvegicus
L242DLRHSLMPMLE1Mus musculus
L243LRQGLLPVLES4Homo sapiens, Bos taurus, Pan troglodytes, Macaca mulatta
L243LQTRMEPYMEN1Danio rerio
L243FRERLTPYAEN1Gallus gallus
L243LGQGLMPVLEA1Rattus norvegicus
L243LRHSLMPMLET1Mus musculus
L246GLLPVLESFKV3Homo sapiens, Pan troglodytes, Macaca mulatta
L246RMEPYMENVRT1Danio rerio
L246RLTPYAENLKN1Gallus gallus
L246GLLPVLESLKV1Bos taurus
L246GLMPVLEAWKA1Rattus norvegicus
L246SLMPMLETLKT1Mus musculus
N208EALKENGGARL3Homo sapiens, Pan troglodytes, Macaca mulatta
N208EDLRTMAAPYA1Danio rerio
N208EEIREKGIPQA1Gallus gallus
N208EALKEGGGS-L1Bos taurus
N208TEIKNH--PTL1Rattus norvegicus
N208AELKSN--PTL1Mus musculus
Q196SDELRQRLAAR3Homo sapiens, Pan troglodytes, Macaca mulatta
Q196VEAVRTKLTER1Danio rerio
Q196SDELRQKLSQK1Gallus gallus
Q196SDDLRQRLTAR1Bos taurus
Q196SDQMRENLAQR1Rattus norvegicus
Q196SEQMRESLAQR1Mus musculus
R195YSDELRQRLAA3Homo sapiens, Pan troglodytes, Macaca mulatta
R195MVEAVRTKLTE1Danio rerio
R195YSDELRQKLSQ1Gallus gallus
R195YSDDLRQRLTA1Bos taurus
R195YSDQMRENLAQ1Rattus norvegicus
R195HSEQMRESLAQ1Mus musculus
R212ENGGARLAEYH3Homo sapiens, Pan troglodytes, Macaca mulatta
R212TMAAPYAEEYK1Danio rerio
R212EKGIPQASEYQ1Gallus gallus
R212EGGGS-LAEYH1Bos taurus
R212NH--PTLIEYH1Rattus norvegicus
R212SN--PTLNEYH1Mus musculus
Y260SALEEYTKKLN2Homo sapiens, Pan troglodytes
Y260QMYETIAKAIQ1Danio rerio
Y260SFLDELQKSVA1Gallus gallus
Y260AAIDEASKKLN1Bos taurus
Y260SALEEYTKKLS1Macaca mulatta
Y260SMIDEAKKKLN1Rattus norvegicus
Y260SVIDKASETLT1Mus musculus


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