Table 3.
Summary of the top-15 hotspots detected by GGDL
| ID | Sizea | Locib | GOc | Hitsd | GDL (all)e | GDL (hits)f | G-Lasso(all)g | G-Lasso(hits)h | SIOL(all)i | SIOL(hits)j | LORS(all)k | LORS(hits)l |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 31 | XII:1056097 | (1)*** | 7 | 31 | 7 | 32 | 7 | 8 | 6 | 31 | 7 |
| 2 | 28 | III:81832..92391 | (2)** | 5 | 29 | 5 | 28 | 5 | 58 | 5 | 22 | 4 |
| 3 | 28 | XII:1056103 | (1)*** | 7 | 29 | 6 | 28 | 6 | 1 | 1 | 2 | 0 |
| 4 | 27 | III:79091 | (2)*** | 6 | 29 | 6 | 28 | 6 | 28 | 7 | 10 | 2 |
| 5 | 27 | III:175799..177850 | (3)* | 3 | 26 | 3 | 23 | 3 | 9 | 2 | 18 | 4 |
| 6 | 27 | XII:1059925..1059930 | (1)*** | 7 | 27 | 7 | 27 | 7 | 0 | 0 | 5 | 1 |
| 7 | 25 | III:105042 | (2)*** | 6 | 23 | 6 | 25 | 6 | 5 | 3 | 19 | 4 |
| 8 | 23 | III:201166..201167 | (3)*** | 3 | 23 | 3 | 22 | 3 | 13 | 2 | 23 | 3 |
| 9 | 22 | XII:1054278..1054302 | (1)*** | 7 | 26 | 7 | 24 | 7 | 24 | 5 | 12 | 4 |
| 10 | 21 | III:100213 | (2)** | 5 | 23 | 5 | 23 | 5 | 5 | 3 | 5 | 1 |
| 11 | 20 | III:209932 | (3)* | 3 | 21 | 3 | 19 | 3 | 16 | 4 | 15 | 4 |
| 12 | 20 | XII:659357..662627 | (4)* | 4 | 19 | 4 | 3 | 0 | 37 | 9 | 36 | 6 |
| 13 | 19 | III:210748..210748 | (5)* | 4 | 24 | 4 | 18 | 4 | 2 | 3 | 11 | 4 |
| 14 | 19 | VIII:111679..111680 | (6)* | 3 | 20 | 3 | 19 | 3 | 3 | 3 | 12 | 2 |
| 15 | 19 | VIII:111682..111690 | (7)** | 5 | 21 | 5 | 20 | 5 | 57 | 6 | 22 | 3 |
| Total hits | 75 | 74 | 70 | 59 | 49 | |||||||
aNumber of genes associated with the hotspot bThe chromosome position of the hotspot. cThe most significant GO category enriched with the associated gene set. The enrichment test was performed using DAVID (Huang et al., 2009). The gene function is defined by GO category. The involved GO categories are: (i) telomere maintenance via recombination; (ii) branched chain family amino acid biosynthetic process; (iii). regulation of mating-type specific transcription, DNA-dependent; (iv) sterol biosynthetic process; (v) pheromone-dependent signal transduction involved in conjugation with cellular fusion; (vi) cytogamy; (vii) response to pheromone. dNumber of genes that have enriched GO categories. e,g,I,kNumber of associated genes that can also be identified using GDL, G-Lasso, SIOL and LORS, respectively. f,h,j,lNumber of genes that have enriched GO categories and can also be identified by GDL, G-Lasso, SIOL and LORS, respectively. Among these hotspots, hotspot (12) in bold cannot be detected by G-Lasso. Hotspot (6) in italic cannot be detected by SIOL. Hotspot (3) in teletype cannot be detected by LORS. Adjusted P-values using permutation tests. *10–2∼10−3, **10−3∼10−5, ***10−5∼10−10.