Ossification of the posterior longitudinal ligament related genes identification using microarray gene expression profiling and bioinformatics analysis

Hailong He; Lingzhou Mao; Peng Xu; Yanhai Xi; Ning Xu; Mingtao Xue; Jiangming Yu; Xiaojian Ye

doi:10.1016/j.gene.2013.09.001

Ossification of the posterior longitudinal ligament related genes identification using microarray gene expression profiling and bioinformatics analysis

Gene. 2014 Jan 10;533(2):515-9. doi: 10.1016/j.gene.2013.09.001. Epub 2013 Sep 18.

Authors

Hailong He¹, Lingzhou Mao, Peng Xu, Yanhai Xi, Ning Xu, Mingtao Xue, Jiangming Yu, Xiaojian Ye

Affiliation

¹ Department of Orthopaedics, Changzheng Hospital, The Second Military Medical University, No. 415, Fengyang Road, Huangpu District, Shanghai 200003, China. Electronic address: hailonghe@hotmail.com.

PMID: 24055420
DOI: 10.1016/j.gene.2013.09.001

Abstract

Ossification of the posterior longitudinal ligament (OPLL) is a kind of disease with physical barriers and neurological disorders. The objective of this study was to explore the differentially expressed genes (DEGs) in OPLL patient ligament cells and identify the target sites for the prevention and treatment of OPLL in clinic. Gene expression data GSE5464 was downloaded from Gene Expression Omnibus; then DEGs were screened by limma package in R language, and changed functions and pathways of OPLL cells compared to normal cells were identified by DAVID (The Database for Annotation, Visualization and Integrated Discovery); finally, an interaction network of DEGs was constructed by string. A total of 1536 DEGs were screened, with 31 down-regulated and 1505 up-regulated genes. Response to wounding function and Toll-like receptor signaling pathway may involve in the development of OPLL. Genes, such as PDGFB, PRDX2 may involve in OPLL through response to wounding function. Toll-like receptor signaling pathway enriched genes such as TLR1, TLR5, and TLR7 may involve in spine cord injury in OPLL. PIK3R1 was the hub gene in the network of DEGs with the highest degree; INSR was one of the most closely related genes of it. OPLL related genes screened by microarray gene expression profiling and bioinformatics analysis may be helpful for elucidating the mechanism of OPLL.

Keywords: BH; BMP-2; Benjamin and Hochberg; DAVID; DEGs; Differentially expressed gene; Dysfunctional pathway; ESR2; FC; FDR; GO; Gene Ontology; INSR; KEGG; Kyoto Encyclopedia Genes and Genomes; MAPK10; OPLL; Ossification of the posterior longitudinal ligament; PDGFB; PI3K; PIK3R1; PRDX2; Phosphoinositide 3-kinase; TLR 1; TLRs; The Database for Annotation, Visualization and Integrated Discovery; Toll-like receptor 1; Toll-like receptors; bone morphogenetic protein 2; differentially expressed genes; estrogen receptor 2; false discovery rate; fold chance; insulin receptor; mitogen-activated protein kinases 10; ossification of the posterior longitudinal ligament; peroxiredoxin 2; phosphoinositide-3-kinase, regulatory subunit 1; platelet-derived growth factor-B.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cluster Analysis
Computational Biology
Gene Expression Profiling
Gene Regulatory Networks
Genetic Association Studies
Humans
Metabolic Networks and Pathways / genetics
Microarray Analysis
Ossification of Posterior Longitudinal Ligament / genetics*