modENCODE Copy Number Variation Data
This spreadsheet is one worksheet from Supplemental Table 2 of Hangnoh Lee, C. Joel McManus, Dong-Yeon Cho, Matthew Eaton, Fioranna Renda, Maria Patrizia Somma, Lucy Cherbas, Gemma May, Sara Powell, Dayu Zhang, Lijun Zhan, Alissa Resch, Justen Andrews, Susan Celniker, Peter Cherbas, Teresa Przytycka, Maurizio Gatti, Brian Oliver, Brenton Graveley, and David MacAlpine (2014): DNA copy number evolution in Drosophila, Genome Biology 2014, 15(8):R70. In a few cases, DNA-seq was carried out independent in more than one of the participating laboratories; in these cases both data sets are shown in the spreadsheet, distinguished by the initials of the lab PI. The rows represent 1 kb windows covering the entire genome. The columns are defined as follows:
| Chromosome (arms) | Drosophila chromosome arms based on the reference genome (Release 5) |
|---|---|
| Start | Base positions where 1kb windows start from |
| "Cell Line Name"_CopyNumber Copy | number of the 1kb window |
| "Cell Line Name"_Call | Information of Gain or Loss of DNA copy |
| HighCopyHits | Number of cell lines that are called as "High Copy" (= gain) for the window |
| LowCopyHits | Number of cell lines that are called as "Low Copy" (= loss) for the window |
| p value HighCopyHits | p value of HighCopyHits of the window that is determined by a permutation test |
| p value LowCopyHits | p value of LowCopyHits of the window that is determined by a permutation test |
| q value HighCopyHits | FDR corrected p values for HighCopyHits (FDR : False Discovery Rate) |
| q value LowCopyHits | FDR corrected p values for HighCopyHits (FDR : False Discovery Rate) |
