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Table 1 Assessing cross-hybridization using pseudogenes

From: Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

   Tiling Array   
   lower equal higher non-expr total fraction
RNA-seq lower 43 24 0 4 71 0.28
  equal 0 1 1 0 2 0.01
  higher 1 4 11 2 18 0.07
  non-expr 12 11 11 133 167 0.65
  total 56 40 23 139 258 1.00
  fraction 0.22 0.16 0.09 0.54 1.00  
   (a)   
   Tiling Array   
   lower equal higher non-expr total fraction
RNA-seq lower 28 12 1 4 45 0.21
  equal 0 2 0 0 2 0.01
  higher 0 3 6 0 9 0.04
  non-expr 8 36 12 100 156 0.74
  total 36 53 19 104 212 1.00
  fraction 0.17 0.25 0.09 0.49 1.00  
   (b)   
  1. (a) The total row (column) gives the number of duplicated pseudogene-gene parent pairs from the tiling array (RNA-Seq) data where the relative expression level of the duplicated pseudogene is lower, equal, or higher than its parent gene. Non-expr means neither the pseudogene nor its parent are expressed. The equal and higher cases are indicative of cross-hybridization because the pseudogene, which is similar in sequence to its parent gene, is found to be expressed although most pseudogenes are believed not to be. The overlap between the two platforms is also shown for each combination of categories. For example, out of the 56 and 71 cases where the pseudogene's expression is lower than its parent gene for tiling array and RNA-Seq, respectively, 43 of the pseudogene-gene pairs are in common. (b) Similar results for processed pseudogenes.