The assignment process for pseudogenes is described in detail by Pei et al. (2012). Briefly, in silico identification of pseudogenes is obtained from routine implementation of Yale's Pseudopipe (Zhang et al. 2006) with every new release of Ensembl. Pseudopipe identified 18,046 pseudogenes based on the human genome release in Ensembl 61. These pseudogenes were compared to a recent run of UCSC's RetroFinder, which included 13,644 pseudogenes, and HAVANA's latest annotations of 11,224 pseudogenes based on GENCODE 7, level 2. A three-way Yale, UCSC, and HAVANA pseudogene consensus set was obtained by using an overlap criteria of 50 bp and was developed for the annotation of 1% ENCODE Regions (Zheng et al. 2007). This resulted in a consensus set of 7183 pseudogenes, which are tagged level 1. The functional paralog of a pseudogene is often referred to as the “parent” gene. Currently, we have successfully identified parents for 9369 pseudogenes of the manually annotated pseudogenes, whereas the parents for the remaining 1847 pseudogenes are still ambiguous and may require further investigation. It is important to note, however, that it is not
