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 APCS
Gene summary
Basic gene Info.Gene symbolAPCS
Gene nameamyloid P component, serum
SynonymsHEL-S-92n|PTX2|SAP
CytomapUCSC genome browser: 1q21-q23
Type of geneprotein-coding
RefGenesNM_001639.3,
Description9.5S alpha-1-glycoproteinepididymis secretory sperm binding protein Li 92npentaxin-relatedserum amyloid P-component
Modification date20141207
dbXrefs MIM : 104770
HGNC : HGNC
Ensembl : ENSG00000132703
HPRD : 00101
Vega : OTTHUMG00000022741
ProteinUniProt: P02743
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APCS
BioGPS: 325
PathwayNCI Pathway Interaction Database: APCS
KEGG: APCS
REACTOME: APCS
Pathway Commons: APCS
ContextiHOP: APCS
ligand binding site mutation search in PubMed: APCS
UCL Cancer Institute: APCS
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0044869negative regulation by host of viral exo-alpha-sialidase activity23544079
GO:0044871negative regulation by host of viral glycoprotein metabolic process23544079
GO:0045087innate immune response23544079
GO:0045656negative regulation of monocyte differentiation14607961
GO:0046597negative regulation of viral entry into host cell23544079
GO:0048525negative regulation of viral process23544079
GO:1903016negative regulation of exo-alpha-sialidase activity23544079
GO:1903019negative regulation of glycoprotein metabolic process23544079


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Ligand binding site mutations for APCS

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
D157Y159CHNSC1
Y93S91CLUAD1
K98H97QLUAD1
K98T100ILUAD1
S120S121LLUSC1
E118E118VOV1
S181D180EOV1
S120S121LSKCM1
E210E210KSKCM1
D157D157NSKCM1
Q167F169SUCEC1
K162G160EUCEC1
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 APCS
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
S120S121L0.35949818
E210E210K-1.0307416
Q167F169S-0.87855821
D157Y159C-0.87117141
K98T100I-0.77979788
D157D157N-0.74484373
E118E118V-0.71426961
K98H97Q-0.59112364
Y93S91C-0.52790446
K162G160E-0.48641223
S181D180E-0.37697513
(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 APCS from PDB

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Differential gene expression and gene-gene network for APCS
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 APCS and the right PPI network was created from samples without mutations in the LBS of APCS. 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 APCS
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C2239176Carcinoma, Hepatocellular2Biomarker
umls:C1956346Coronary Artery Disease2Biomarker
umls:C0018801Heart Failure1Biomarker
umls:C0023903Liver Neoplasms1Biomarker

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

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Pharmacological information for APCS
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
ExperimentalDB01651Methyl 4,6-O-[(1r)-1-Carboxyethylidene]-Beta-D-GalactopyranosideSmall molecule
ExperimentalDB07579BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANESmall molecule
ExperimentalDB07580BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINESmall molecule

Gene-centered ligand-gene interaction network

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


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Conservation information for LBS of APCS
Multiple alignments for P02743 in multiple species
LBSAA sequence# speciesSpecies
D157LGQEQDSYGGK1Homo sapiens
D157LGQEQDNYGGG1Mus musculus
D157LGQEQDTYGGG1Rattus norvegicus
D157LGQEQDSYGGG1Bos taurus
D164YGGKFDRSQSF1Homo sapiens
D164YGGGFQRSQSF1Mus musculus
D164YGGGFDKTQSF1Rattus norvegicus
D164YGGGFDKNQSF1Bos taurus
D77NTQGRDNELLV1Homo sapiens
D77SVKGRDNELLI1Mus musculus
D77SVNSRDNELLI1Rattus norvegicus
D77NIHSKDNELLV1Bos taurus
E118ICVSWESSSGI1Homo sapiens
E118LCTTWESSSGI1Mus musculus
E118FCTSWESSSGI1Rattus norvegicus
E118ICTSWESSTGI1Bos taurus
E155IVLGQEQDSYG2Homo sapiens, Bos taurus
E155IVLGQEQDNYG1Mus musculus
E155IVLGQEQDTYG1Rattus norvegicus
E210QALNYEIRGYV1Homo sapiens
E210QALNYEINGYV1Mus musculus
E210RALNYEINGYV1Rattus norvegicus
E210QALKYEIKGYV1Bos taurus
F163SYGGKFDRSQS1Homo sapiens
F163NYGGGFQRSQS1Mus musculus
F163TYGGGFDKTQS1Rattus norvegicus
F163SYGGGFDKNQS1Bos taurus
I211ALNYEINGYVV2Mus musculus, Rattus norvegicus
I211ALNYEIRGYVI1Homo sapiens
I211ALKYEIKGYVI1Bos taurus
K162DSYGGKFDRSQ1Homo sapiens
K162DNYGGGFQRSQ1Mus musculus
K162DTYGGGFDKTQ1Rattus norvegicus
K162DSYGGGFDKNQ1Bos taurus
K98YIGRHKVTSKV1Homo sapiens
K98YIGQSKVTVRG1Mus musculus
K98YIGNSKVTVRG1Rattus norvegicus
K98YIGKTKVTVRA1Bos taurus
L81RDNELLVYKER1Homo sapiens
L81RDNELLIYKEK1Mus musculus
L81RDNELLIYKDK1Rattus norvegicus
L81KDNELLVFKNG1Bos taurus
N51EKPLQNFTLCF3Homo sapiens, Mus musculus, Rattus norvegicus
N51EKPLKNLTLCL1Bos taurus
N78TQGRDNELLVY1Homo sapiens
N78VKGRDNELLIY1Mus musculus
N78VNSRDNELLIY1Rattus norvegicus
N78IHSKDNELLVF1Bos taurus
Q156VLGQEQDSYGG2Homo sapiens, Bos taurus
Q156VLGQEQDNYGG1Mus musculus
Q156VLGQEQDTYGG1Rattus norvegicus
Q167KFDRSQSFVGE1Homo sapiens
Q167GFQRSQSFVGE1Mus musculus
Q167GFDKTQSFVGE1Rattus norvegicus
Q167GFDKNQSFMGE1Bos taurus
Q50LEKPLQNFTLC3Homo sapiens, Mus musculus, Rattus norvegicus
Q50LEKPLKNLTLC1Bos taurus
R212LNYEINGYVVI2Mus musculus, Rattus norvegicus
R212LNYEIRGYVII1Homo sapiens
R212LKYEIKGYVIV1Bos taurus
S120VSWESSSGIAE1Homo sapiens
S120TTWESSSGIVE1Mus musculus
S120TSWESSSGIAE1Rattus norvegicus
S120TSWESSTGIAE1Bos taurus
S166GKFDRSQSFVG1Homo sapiens
S166GGFQRSQSFVG1Mus musculus
S166GGFDKTQSFVG1Rattus norvegicus
S166GGFDKNQSFMG1Bos taurus
S181LYMWDSVLPPE1Homo sapiens
S181LYMWDYVLTPQ1Mus musculus
S181LYMWDSVLTPE1Rattus norvegicus
S181LYMWDSVLSPE1Bos taurus
V182YMWDSVLPPEN1Homo sapiens
V182YMWDYVLTPQD1Mus musculus
V182YMWDSVLTPEN1Rattus norvegicus
V182YMWDSVLSPEE1Bos taurus
Y209WQALNYEIRGY1Homo sapiens
Y209WQALNYEINGY1Mus musculus
Y209WRALNYEINGY1Rattus norvegicus
Y209WQALKYEIKGY1Bos taurus
Y83NELLVYKERVG1Homo sapiens
Y83NELLIYKEKVG1Mus musculus
Y83NELLIYKDKVG1Rattus norvegicus
Y83NELLVFKNGIG1Bos taurus
Y93GEYSLYIGRHK1Homo sapiens
Y93GEYSLYIGQSK1Mus musculus
Y93GQYSLYIGNSK1Rattus norvegicus
Y93GEYSLYIGKTK1Bos taurus


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