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mutLBSgeneDB |
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| Gene summary for PGLYRP4 |
 Gene summary |
| Basic gene Info. | Gene symbol | PGLYRP4 |
| Gene name | peptidoglycan recognition protein 4 | |
| Synonyms | PGLYRPIbeta|PGRP-Ibeta|PGRPIB | |
| Cytomap | UCSC genome browser: 1q21 | |
| Type of gene | protein-coding | |
| RefGenes | NM_020393.3, | |
| Description | PGRP-I-betapeptidoglycan recognition protein I betapeptidoglycan recognition protein I-betapeptidoglycan recognition protein intermediate betapeptidoglycan recognition protein-I-beta | |
| Modification date | 20141216 | |
| dbXrefs | MIM : 608198 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000163218 | ||
| HPRD : 16298 | ||
| Vega : OTTHUMG00000037057 | ||
| Protein | UniProt: Q96LB8 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PGLYRP4 | |
| BioGPS: 57115 | ||
| Pathway | NCI Pathway Interaction Database: PGLYRP4 | |
| KEGG: PGLYRP4 | ||
| REACTOME: PGLYRP4 | ||
| Pathway Commons: PGLYRP4 | ||
| Context | iHOP: PGLYRP4 | |
| ligand binding site mutation search in PubMed: PGLYRP4 | ||
| UCL Cancer Institute: PGLYRP4 | ||
| 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 | GO:0002221 | pattern recognition receptor signaling pathway | 11461926 | GO:0016045 | detection of bacterium | 11461926 | GO:0050830 | defense response to Gram-positive bacterium | 11461926 |
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| Ligand binding site mutations for PGLYRP4 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | S295 | S295F | SKCM | 2 | H240 | H240Y | SKCM | 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 PGLYRP4 |
| 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 |
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| 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 | S295 | S295F | -0.62197823 | H240 | H240Y | -0.42371317 |
| (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 PGLYRP4 from PDB |
| PDB ID | PDB title | PDB structure | 2EAX | Crystal structure of human PGRP-IBETAC in complex with glycosamyl muramyl pentapeptide |  |
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| Differential gene expression and gene-gene network for PGLYRP4 |
| 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) |
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| Phenotype information for PGLYRP4 |
| 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 PGLYRP4 |
| 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PGLYRP4 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | AMV | METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE | 2eax | C | H240 | III | Peptide ligand (ALA,FGA,LYS,DAL,DAL) | 2eax | C | S295 |
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| Conservation information for LBS of PGLYRP4 |
| Multiple alignments for Q96LB8 in multiple species |
| LBS | AA sequence | # species | Species | D301 | HAAEWNPYSIG | 2 | Drosophila melanogaster, Drosophila melanogaster | D301 | STPGYDDIALG | 1 | Homo sapiens | D301 | HATNWNSKSIG | 1 | Drosophila melanogaster | D302 | AAEWNPYSIGI | 2 | Drosophila melanogaster, Drosophila melanogaster | D302 | TPGYDDIALGI | 1 | Homo sapiens | D302 | ATNWNSKSIGI | 1 | Drosophila melanogaster | G299 | GAHAAEWNPYS | 2 | Drosophila melanogaster, Drosophila melanogaster | G299 | GSSTPGYDDIA | 1 | Homo sapiens | G299 | GAHATNWNSKS | 1 | Drosophila melanogaster | H240 | --IIHHTAGSY | 2 | Drosophila melanogaster, Drosophila melanogaster | H240 | YGIIIHTAGRT | 1 | Homo sapiens | H240 | --VIHHTAGNY | 1 | Drosophila melanogaster | K268 | HMDSLGWPDIG | 2 | Drosophila melanogaster, Drosophila melanogaster | K268 | YIDRLKSCDIG | 1 | Homo sapiens | K268 | HMDSLGWADIG | 1 | Drosophila melanogaster | P298 | MGAHAAEWNPY | 2 | Drosophila melanogaster, Drosophila melanogaster | P298 | QGSSTPGYDDI | 1 | Homo sapiens | P298 | MGAHATNWNSK | 1 | Drosophila melanogaster | S295 | WNNMGAHAAEW | 2 | Drosophila melanogaster, Drosophila melanogaster | S295 | WNVQGSSTPGY | 1 | Homo sapiens | S295 | WNVMGAHATNW | 1 | Drosophila melanogaster | S296 | NNMGAHAAEWN | 2 | Drosophila melanogaster, Drosophila melanogaster | S296 | NVQGSSTPGYD | 1 | Homo sapiens | S296 | NVMGAHATNWN | 1 | Drosophila melanogaster | T241 | -IIHHTAGSYC | 2 | Drosophila melanogaster, Drosophila melanogaster | T241 | GIIIHTAGRTC | 1 | Homo sapiens | T241 | -VIHHTAGNYC | 1 | Drosophila melanogaster | Y117 | ----------- | 3 | Drosophila melanogaster, Drosophila melanogaster, Drosophila melanogaster | Y117 | GCDVAYNFLVG | 1 | Homo sapiens | Y263 | SVQNYHMDSLG | 2 | Drosophila melanogaster, Drosophila melanogaster | Y263 | DIQSFYIDRLK | 1 | Homo sapiens | Y263 | NIQAYHMDSLG | 1 | Drosophila melanogaster |
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