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Table 3 Association analyses between the differentially expressed genes (DEGs) in ASD and the human Alu-inserted gene lists

From: Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder

Insertion type Comparison GEO datasets All differentially expressed genes Upregulated genes Downregulated genes
P value Genes (n) P value Genes (n) P value Genes (n)
All insertion ASD vs. control GSE15402 0.799 215 0.926 100 0.799 116
GSE18123 < 0.00005 1492 1.000 255 < 0.00005 1245
GSE25507 0.012 869 0.256 522 < 0.00005 355
GSE42133 < 0.00005 1001 0.015 387 < 0.00005 624
GSE6575 < 0.00005 388 0.955 123 < 0.00005 266
Intronic ASD vs. control GSE15402 0.784 212 0.926 99 0.784 114
GSE18123 < 0.00005 1476 0.970 252 < 0.00005 1231
GSE25507 0.007 860 0.322 516 < 0.00005 352
GSE42133 < 0.00005 985 0.012 382 < 0.00005 613
GSE6575 < 0.00005 382 0.882 119 < 0.00005 264
Exonized ASD vs. control GSE15402 1.000 15 0.933 6 0.933 9
GSE18123 0.009 102 0.926 14 0.003 88
GSE25507 0.825 45 0.008 17 0.012 28
GSE42133 0.008 75 0.306 27 0.015 49
GSE6575 0.006 33 1.000 7 < 0.00005 26
Exonic ASD vs. control GSE15402 0.450 19 0.904 10 0.426 9
GSE18123 0.001 177 0.306 21 < 0.00005 158
GSE25507 0.426 78 0.136 46 0.662 33
GSE42133 < 0.00005 148 0.799 43 < 0.00005 106
GSE6575 0.034 48 0.715 16 0.013 33
Promoter ASD vs. control GSE15402 0.933 6 0.436 1 0.799 5
GSE18123 0.240 37 0.898 8 0.268 29
GSE25507 0.135 22 0.033 11 0.937 11
GSE42133 0.831 35 0.447 19 0.255 16
GSE6575 0.466 16 0.716 3 0.123 13
  1. The list of DEGs from each gene expression profiling study was overlapped with the lists of Alu-inserted genes. Alu-inserted genes were categorized into five types of Alu insertions which included exonized, exonic, intronic, promoter, and combined insertion types. Fisher’s exact test with Benjamini-Hochberg correction (FDR = 0.05) was used to determine the association the DEGs and Alu-inserted genes, and P values of less than 0.05 were considered significant. The number of DEGs and adjusted P values are shown