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Table 3 Comparison of our bioinformatics results to literature-based gene expression signatures of DNA damage-induced response

From: Gene and protein analysis reveals that p53 pathway is functionally inactivated in cytogenetically normal Acute Myeloid Leukemia and Acute Promyelocytic Leukemia

Ref System Literature-based gene signature Our bionformatic results
   Number of genes altered in the signature Number of genes included in our p53 list DEGs in CN-AML DEGs in APL
[85] p53-dependent transcriptional response of cell lines to 9 DNA-damaging agents 16 ↑ 12↑ 0 ↑ 1 ↓ 0↑ 1 ↓
[86] transcriptional response of human cells to ionizing radiation 199 ↑ 49 ↓ 59 ↑ 11 ↓ 1↑ 6↓ 1↑ 7↓
[87] healthy PB cells irradiated ex vivo 61a 29 3 5
[88] 34 patients before and after irradiationb 23a 12 1 1
[89] 7 AML patients before and after chemotherapyc 30↑ [113 ↑]d 29↑ 1↑ 2↓ 0↑ 3↓
  Total   152 33/152 DEGs, 119/152 not DEGs
  1. We compare how many of upregulated/downregulated genes in the signature are indeed upregulated or downregulated DEGs in our analysis of CN-AML and APL, ↑- upregulated gene expression, ↓- downregulated gene expression
  2. aOnly the list of the signature genes was provided, without the specific names of up- and down-regulated genes. Therefore, we present the overall number of upregulated and downregulated DEGs
  3. bAll are hematological patients
  4. c5 are CN-AML patients and 1 is APL
  5. d30 of the upregulated 113 genes are associated with p53 regulation