title: Gene co-expression network and function modules in three types of glioma.
abstract: The aim of the present study was to identify the disease‑associated genes and their functions involved in the development of three types of glioma (astrocytoma, glioblastoma and oligodendroglioma) with DNA microarray technology, and to analyze their differences and correlations. First, the gene expression profile GSE4290 was downloaded from the Gene Expression Omnibus database, then the probe‑level data were pre‑processed and the differentially expressed genes (DEGs) were identified with limma package in R language. Gene functions of the selected DEGs were further analyzed with the Database for Annotation, Visualization and Integrated Discovery. After the co‑expression network of DEGs was constructed by Cytoscape, the functional modules were mined and enrichment analysis was performed, and then the similarities and differences between any two types of glioma were compared. A total of 1151 genes between normal and astrocytoma tissues, 684 genes between normal and malignant glioma tissues, and 551 genes between normal and oligodendroglioma tissues were filtered as DEGs, respectively. By constructing co‑expression networks of DEGs, a total of 77232, 455 and 987 interactions were involved in the differentially co‑expressed networks of astrocytoma, oligodendroglioma and glioblastoma, respectively. The functions of DEGs were consistent with the modules in astrocytoma, glioblastoma and oligodendroglioma, which were mainly enriched in neuron signal transmission, immune responses and synthesis of organic acids, respectively. Model functions of astrocytoma and glioblastoma were similar (mainly related with immune response), while the model functions of oligodendroglioma differed markedly from that of the other two types. The identification of the associations among these three types of glioma has potential clinical utility for improving the diagnosis of different types of glioma in the future. In addition, these results have marked significance in studying the underlying mechanisms, distinguishing between normal and cancer tissues, and examining novel therapeutic strategies for patients with glioma.
authors.affiliation: Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China.
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.affiliation: Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China.
authors.forename: Weiran
authors.initials: W
authors.lastname: Pan
authors.affiliation: Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China.
authors.forename: Xiaoxiao
authors.initials: X
authors.lastname: Yang
authors.affiliation: Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China.
authors.forename: Jinming
authors.initials: J
authors.lastname: Miao
mesh_terms: D001254:Astrocytoma / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D057225:Data Mining; D030561:Databases, Nucleic Acid; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D005909:Glioblastoma / Q000235:genetics / Q000378:metabolism; D005910:Glioma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D006801:Humans; D058977:Molecular Sequence Annotation; D009837:Oligodendroglioma / Q000235:genetics / Q000378:metabolism