These genes are likely to play a central role in regulating the biological process of BM regeneration and promote organisms to recover from IR injury. In our present experiments, we focused on the stage of BM regeneration, from the increase of the number of BMNCs at 3 DAI to 21 DAI, rather than irradiation-induced injury phase, which occurs AZD2281 within several hours after IR. Microarray analysis of irradiated mice at the recovery phase has not been report so far. Dai et al. reported that in murine BM 6 h after 6.5 Gy gamma irradiation, the functional categories of differentially expressed genes are comprised of biological processes including DNA replication/repair, proliferation/apoptosis, cell cycle control and RNA processing . Therefore, we can conclude that the responses of irradiated bone marrow tissue are different at the stage of injury compared to recovery. For example, p53 and its downstream target genes which induce cell-cycle arrest, DNA repair and apoptosis are up-regulated after IR , but we observed no expression change of these genes during the recovery phase in our experiment. Microarray analysis is an effective technique to simultaneously compare the global gene expression between experimental and control groups. However, high-throughput data are generally of high variability, low reproducibility and contain non-specific noise , where subgroups of genes within the dataset may be associated with a generalized response to a given stimulus. This effect can be ameliorated using a comprehensive text mining and bioinformatics approach including: STEM cluster analysis, GO analysis, Dynamic Gene Network analysis and DAVID pathway analysis as an effective method to enrich the most relevant IR responsive genes. STEM cluster analysis was performed for clustering and comparing the 1302 differentially expressed genes to depict the dynamic changes in these genes and their relationships to irradiation stimulus. Genes in the same temporal expression profiles are more likely to be grouped in certain pathways, or have common biological processes . As shown in Table S3, we found that genes contained in the same temporal expression pattern share similar functionality. For example, profile 0 comprises 64 differentially expressed genes, with GO enrichment in immune response and cellular component organization. Integrated results of GO analysis and cluster analysis suggest that immune response , response to stimuli, cellular processes and signaling processes are the most critical GO terms related to IR, especially for immune response at the recovery phase of IR.