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

BMC Genomics

Table 1 Assessing cross-hybridization using pseudogenes

(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.

ISSN: 1471-2164