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1 This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content".
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2 In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding
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3 fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream
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4 of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements,
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5 used as control in the test. The regions are aligned around their center (i.e. around the ETn integration
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6 sites).
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7 Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In
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8 particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination
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9 hotspots curve made of 64 values. The measurement used is the feature content, i.e. the
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10 fraction of the 1-kb window that is covered by recombination hotspots
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11
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12 Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F
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13 Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse
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14 endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology.
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15 12(6): 1-41.
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16 Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL
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17 Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two
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18 active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007.
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19 Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams,
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20 B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse
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21 genome. Genetics. 191: 757-764. |
