A wide range of biotic stresses (BS) and abiotic stresses (AS) adversely affect plant growth and productivity worldwide. The study of individual genes cannot be considered as an effective approach for the understanding of tolerance mechanisms, since these stresses are frequent and often in combination with each other, and a large number of genes are involved in these mechanisms. The availability of high-throughput genomic data has enabled the discovery of the role of transcription factors (TFs) in regulatory networks. A meta-analysis of BS and AS responses was performed by analyzing a total of 391 microarray samples from 23 different experiments and 2,336 differentially expressed genes (DEGs) involved in multiple stresses were identified. We identified 1,862 genes differentially regulated in response to BS was much greater than that regulated by AS, 835 genes, and found 15.4% or 361 DEGs with the conserved expression between AS and BS. The greatest percent of genes related to the cellular process (>76% genes), metabolic process (>76% genes) and response to stimulus (>50%). About 4.2% of genes involved in BS and AS responses belonged to the TF families. We identified several genes, which encode TFs that play an important role in AS and BS responses. These proteins included Jasmonate Ethylene Response Factor 1 (JERF1), SlGRAS6, MYB48, SlERF4, EIL2, protein LATE ELONGATED HYPOCOTYL (LHY), SlERF1, WRKY 26, basic leucine zipper TF, inducer of CBF expression 1-like, pti6, EIL3 and WRKY 11. Six of these proteins, JERF1, MYB48, protein LHY, EIL3, EIL2 and SlGRAS6, play central roles in these mechanisms. This research promoted a new approach to clarify the expression profiles of various genes under different conditions in plants, detected common genes from differentially regulated in response to these conditions and introduced them as candidate genes for improving plant tolerance through genetic engineering approach.