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Table 2 Enrichment analysis of individual elements in three cell types. Significant changes (p.adjusted < 0.05) between the donors and IPF patients in the WL, AT2 and AM are shown

From: The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

  Differential expression No differential expression Total in the genome Fisher exact test of enrichment
WL
 LINE 4 179 183 0.75
 LTR 11 577 588 0.75
 SINE 0 63 63 0.61
AT2
 LINE 19 164 183 0.56
 LTR 57 531 588 0.69
 SINE 2 61 63 0.11
AM
 LINE 1 182 183 0.31
 LTR 11 577 588 0.36
 SINE 1 62 63 1.00
  1. The TE changes are shown at the family level whereas each number represents number of TEs subfamily changes. WL whole lung, AT2 alveolar type II cell, AM alveolar macrophage. Enrichment analysis of individual families was performed using Fisher exact test where each family was tested against the sum of other families for each cell type. BH adjusted p-values are shown. Only LINE, SINE and LTR families were considered