Analysis of TCGA data of genes and key pathways indicates potential role of histones in breast cancer

Backgrounds: Protein-protein interactions (PPI) are very important in understanding theregulatory processes involved in cancer.Materials and Methods: The TCGAbiolinks package was used to obtain RNASeq geneexpression data of breast cancer (BC). The data were normalized using the Trimmed Mean of Mvalues(TMM) normalization approach. Then, limma package was used to find DEGs betweentumor samples and normal breast tissues. The STRING database was used for the construction ofthe PPI network for up-and down-regulated genes separately. MCODE App was used to analysisthe networks as well as ClueGo and Cluepedia Apps in cytoscape software were used forfunctional annotations of networks.Results: The gene ontology (GO) analysis of up regulated DEGs indicated their prominent rolesin mitotic cell cycle and chromosome organization. Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis of up regulated DEGs indicated the involvement of the identified genes indifferent pathways involved in cell cycle and oocyte meiosis. Two important clusters of PPI wereidentified. Interestingly, one of the clusters of PPI networks of up regulated genes was found toencode only histone proteins like HIST۱H۴E, HIST۱H۱D, and HIST۲H۴A.Conclusion: The data from this study suggested that the importance of histones gene expressionin breast cancer, which could suggest histone proteins as possible novel prognostic biomarkers inbreast cancer therapy.

Keywords:

TCGA , Breast cancer , PPI network , Histones