Additional file 9.

Regression trees for chromosome 12. (a) The first split (×80) measures the distance between the gene to the nearest full length (FL) Lx4B element (which is uniquely located at approximately 6.5 Mb), followed by the second split (×53) which records the orientation of the nearest FL L1 Md_F2 to the gene (1 = upstream of the gene, -1 = downstream). (There are 35 copies of FL L1 Md_F2 on chromosome 12 altogether.) The regression tree suggests that the gene silencing effect would be the strongest for a given gene not more than 18.89 Mb away from the FL Lx4B element, (in other words, in the proximal 25.5 Mb of the chromosome), with the nearest FL L1 Md_F2 element being downstream of the gene. (b) When estimated on a subset of genomic features, the regression tree modelled the gene silencing effect differently. Here the gene silencing effect is the strongest for genes with a relatively low local SINE density (≤ 14.5%) and not associated with the core of a large low L1 density (LL1) domain (×34 = 0). Note that genes located in the centre of a large LL1 domain have a median downregulation level of just 10% (node 4 of the tree), which is a very mild effect. Additional file 4 gives details on genomic feature definition.

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Tang et al. Epigenetics & Chromatin 2010 3:10   doi:10.1186/1756-8935-3-10