Research Papers:

Exploring the key genes and pathways in enchondromas using a gene expression microarray

Zhongju Shi, Hengxing Zhou, Bin Pan, Lu Lu, Yi Kang, Lu Liu, Zhijian Wei and Shiqing Feng _

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Oncotarget. 2017; 8:43967-43977. https://doi.org/10.18632/oncotarget.16700

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Zhongju Shi1,*, Hengxing Zhou1,*, Bin Pan1,*, Lu Lu1, Yi Kang1, Lu Liu1, Zhijian Wei1 and Shiqing Feng1

1Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China

*These authors have contributed equally to this work

Correspondence to:

Shiqing Feng, email: [email protected]

Keywords: enchondromas, microarray, differentially expressed genes, pathways, protein–protein interaction

Received: December 01, 2016     Accepted: March 06, 2017     Published: March 30, 2017


Enchondromas are the most common primary benign osseous neoplasms that occur in the medullary bone; they can undergo malignant transformation into chondrosarcoma. However, enchondromas are always undetected in patients, and the molecular mechanism is unclear. To identify key genes and pathways associated with the occurrence and development of enchondromas, we downloaded the gene expression dataset GSE22855 and obtained the differentially expressed genes (DEGs) by analyzing high-throughput gene expression in enchondromas. In total, 635 genes were identified as DEGs. Of these, 225 genes (35.43%) were up-regulated, and the remaining 410 genes (64.57%) were down-regulated. We identified the predominant gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were significantly over-represented in the enchondromas samples compared with the control samples. Subsequently the top 10 core genes were identified from the protein-protein interaction (PPI) network. The enrichment analyses of the genes mainly involved in two significant modules showed that the DEGs were principally related to ribosomes, protein digestion and absorption, ECM-receptor interaction, focal adhesion, amoebiasis and the PI3K-Akt signaling pathway.

Together, these data elucidate the molecular mechanisms underlying the occurrence and development of enchondromas and provide promising candidates for therapeutic intervention and prognostic evaluation. However, further experimental studies are needed to confirm these results.

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