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Selenium deficiency is one of the most prevalent micronutrient deficiencies in the global health issues. Hence, in this investigation, we aimed to explore the key genes and biological pathways associated with selenium deficiency linked with selenium status. Chickens were fed a basal diet, a selenium-deficient diet for 10 weeks. The integrated analysis discovered differential expressed genes between the selenium-deficient and normal samples. Multiple approaches, includes GO analysis (g: Profilers database) and pathway analysis (KEGGs), were employed to functionally annotate the DEGs through R program. The protein-protein interactions (PPI) network, and their visualization, gene cluster, hub genes were identified through the STRING, Cytoscape plugin MCODE, CytoHubba, and CancerGeneNet tool. Our results revealed that administration of selenium-deficient diet markedly reduced plasma selenium concentration. Next, a total of 10,266 DEGs (213 upregulated and 237 downregulated) were identified. GO and KEGGs pathway showed that regulation of cell functions, and cancer pathways. Cytoscape demonstrated that eight modules, ten significant hub genes and CancerGeneNet tool revealed that all hub genes were involved in tumorigenesis pathways. Overall, our investigation offered ten hub genes that could be used as precise diagnostic and prognostic candidate biomarkers of selenium-deficiency might be used as treatment strategy in animal and humans.