title: Gene function analysis in osteosarcoma based on microarray gene expression profiling.
abstract: Osteosa rcoma is an aggressive malignant neoplasm that exhibits osteoblastic differentiation and produces malignant osteoid. The aim of this study was to find feature genes associated with osteosarcoma and correlative gene functions which can distinguish cancer tissues from non-tumor tissues. Gene expression profile GSE14359 was downloaded from Gene Expression Omnibus (GEO) database, including 10 osteosarcoma samples and 2 normal samples. The differentially expressed genes (DEGs) between osteosarcoma and normal specimens were identified using limma package of R. DAVID was applied to mine osteosarcoma associated genes and analyze the GO enrichment on gene functions and KEGG pathways. Then, corresponding protein-protein interaction (PPI) network of DEGs was constructed based on the data collected from STRING datasets. Principal component of top10 DEGs and PPI network of top 20 DEGs were further analyzed. Finally, transcription factors were predicted by uploading the two groups of DEGs to TfactS database. A total of 437 genes, including 114 up-regulated genes and 323 down-regulated genes, were filtered as DEGs, of which 46 were associated with osteosarcoma by Disease Module. GO and KEGG pathway enrichment analysis showed that genes mainly affected the process of immune response and the development of skeletal and vascular system. The PPI network analysis elucidated that hemoglobin and histocompatibility proteins and enzymes, which were associated with immune response, were closely associated with osteosarcoma. Transcription factors MYC and SP1 were predicted to be significantly related to osteosarcoma. The discovery of gene functions and transcription factors has the potential to use in clinic for diagnosis of osteosarcoma in future. In addition, it will pave the way to studying mechanism and effective therapies for osteosarcoma.
authors.affiliation: Department of Orthopedics, First Affiliated Hospital, Zhengzhou University Henan Province, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Department of Cardiology, The First Affiliated Hospital, Zhengzhou University Henan Province, China.
authors.forename: Jinghua
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Orthopedics, First Affiliated Hospital, Zhengzhou University Henan Province, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Tan
authors.affiliation: Department of Orthopedics, First Affiliated Hospital, Zhengzhou University Henan Province, China.
authors.forename: Weidong
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Orthopedics, First Affiliated Hospital, Zhengzhou University Henan Province, China.
authors.forename: Yilin
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Orthopedics, First Affiliated Hospital, Zhengzhou University Henan Province, China.
authors.forename: Ruipeng
authors.initials: R
authors.lastname: Song
authors.affiliation: Department of Orthopedics, First Affiliated Hospital, Zhengzhou University Henan Province, China.
authors.forename: Limin
authors.initials: L
authors.lastname: Wang
keywords: DEGs; GO enrichment; Osteosarcoma; PPI network; transcription factors