For background information, please see: NHGRI: ENCODE Target Selection Process

Stratified Random Picks

To make the stratified picks, the human genome was divided into a top 20%, middle 30%, and bottom 50% stratum along two axes: gene density and non-exonic conservation. Three random picks were taken from each stratum, and a fourth pick was made from the strata that were under-represented in the manual picks. One additional backup pick was made in each stratum as a contingency for unforeseen technical problems within the region. The backup pick is the last (parenthesized) entry listed in each table section.

For an explanation of how gene density and non-exonic conservation were determined, see the Methods section.

Stratification of Manual Picks

The following targets were manually selected as regions of biological interest. See the Methods section for information on strata boundaries.

Semi-Manual Picks

These targets were manually selected from regions that have been extensively studied and help balance the stratification.

Methods

Gene density is defined as the percentage of bases covered either by Ensembl genes or human mRNA best Blat alignments in the UCSC Genome Browser database.

Non-exonic conservation was measured by a fairly elaborate process. 125 base non-overlapping sub-windows were taken inside the 500,000 base windows. Sub-windows with less than 75% of their bases in a mouse alignment were discarded. Of the remaining sub-windows, those with at least 80% base identity were used as the conservation score. To calculate the non-exonic conservation score, the mouse alignments in regions corresponding to the following were discarded: Ensembl genes, all GenBank mRNA Blastz alignments, Fgenesh++ gene predictions, Twinscan gene predictions, spliced EST alignments, and repeats.

The following table shows the non-exonic conservation and gene density of non-overlapping 500 kb regions in the manual picks. The boundaries between strata are:

                          low 50%  middle 30%  high 20%
                          ------------------------------
Gene Density              0.0-1.9%  1.9-4.2%   4.2-100%
Non-Exonic Conservation   0.0-6.3%  6.3-10.6% 10.6-100%