Bioinformatics analysis of promoter genes involved in beef cattle rumen and spleen tissues fed with grass and grain

On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Rumen may function differently in the grass- and grain-fed regimes. Therefore, grain-fed cattle suffer stronger metabolic stress than pasture-fed steers; and they tend to easily have metabolic and infectious diseases. In this study to gain insights into transcriptional regulation in spleen and rumen tissues under two different regimes include grass and grain, the first high expression genes in two different conditions were identified by RNA-seq data analyses. Promoter analysis was performed using a bioinformatics database of Genomatix. Moreover, in this study to the visualization of regulatory networks containing transcription factors and that regulate the genes in the rumen and spleen, were used Cytoscape software. Then, promoter analysis leads to the identification of 31 novel transcription factor activating in the rumen and 10 novel transcription factors candidates in the spleen in cow fed with grass and grains. Results revealed that 10 genes with the highest expression were identified in both rumen and spleen. According to the analysis of the results in the David Database, the processes: reduction of oxidation, regulation of cell proliferation, ion transport, epididymal development ,and ectoderm development were evaluated as significant. The results in this study provide valuable insights into molecular mechanisms in spleen and rumen tissues under two different regimes include grass and grain.