Identification of genes associated with methotrexate resistance in methotrexate-resistant osteosarcoma cell lines

Journal of Orthopaedic Surgery and Research
Xiao-Rong YangRen-Rong Gong

Abstract

This study aimed to better understand the mechanisms underlying methotrexate (MTX)-resistance in osteosarcoma. The raw transcription microarray data GSE16089 collected from three MTX-sensitive osteosarcoma (Saos-2) cell samples and three MTX-resistant osteosarcoma (Saos-2) cell samples were downloaded from Gene Expression Omnibus. After data processing, the differentially expressed genes (DEGs) were identified. Next, DEGs were submitted to DAVID for functional annotation based on the GO (Gene Ontology) database, as well as pathway enrichment analysis based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Transcription factors (TFs) and tumor-associated genes (TAGs) were identified with reference to TRANSFAC and TAG, and TSGene databases, respectively. The protein-protein interaction (PPI) network of the gene-encoded products was constructed, and the subnetwork with the highest score was also detected using Search Tool for the Retrieval of Interacting Genes and BioNet package. A total of 690 up-regulated genes and down-regulated 626 genes were identified. Up-regulated DEGs (including AARS and PARS2) were associated to transfer RNA (tRNA) aminoacylation while down-regulated DEGs (including AURKA, CCNB1, CCNE2, CDK1...Continue Reading

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Citations

Jun 21, 2018·Journal of Orthopaedic Surgery and Research·Yi-Ming RenMeng-Qiang Tian
Jul 1, 2020·International Journal of Molecular Sciences·Martina GodelJoanna Kopecka
Sep 24, 2020·International Journal of Molecular Sciences·Ingrid Lilienthal, Nikolas Herold
Nov 13, 2020·Technology in Cancer Research & Treatment·Fei WangDaliang Kong
Jan 16, 2021·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Jordan AyersMarc Salute

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Datasets Mentioned

BETA
GSE16089

Methods Mentioned

BETA
chips
aminoacylation

Software Mentioned

Gene ID converter
Affy
REACTOME
package
- Package
Cytoscape
BioNet
R
Bioconductor
STRING ( Search Tool for the Retrieval of Interacting Genes

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