Table 1.
Benchmark dataset for software comparison. The 79 artificially modified transcripts in RNA-seq dataset on S. cerevisiae [16] used to generate two artificial datasets (denoted here as Ctrl and Treat) for our software performance comparison study. For each transcript listed in the first column, the specific number of reads listed in the second column is manually added to force differential expression in the Treat group. All the remaining transcripts are left unchanged. Last two columns provide the observed counts as reported by the software.
| Transcript ID | Added | FPKM-Ctrl | FPKM-Treat | Counts-Ctrl | Counts-Treat |
|---|---|---|---|---|---|
| YHR099W | 4 | 7.67 | 8.02 | 42 | 42 |
| YOR096W | 5 | 7,180.96 | 7,163.06 | 1,306 | 1,306 |
| YPL131W | 6 | 3,665.72 | 3,658.45 | 1,645 | 1,645 |
| YJR091C | 10 | 24.82 | 28.1 | 45 | 45 |
| YDR098C | 11 | 239.1 | 255.49 | 86 | 97 |
| YAL042W | 14 | 150.18 | 163.53 | 102 | 116 |
| YKL160W | 20 | 527.66 | 613.6 | 89 | 109 |
| YGR192C | 21 | 21,270.8 | 21,176.2 | 7,392 | 7,413 |
| YGL076C | 22 | 2,797.82 | 2,828.35 | 575 | 575 |
| YER178W | 23 | 580.38 | 600.36 | 348 | 348 |
| YER136W | 24 | 193.87 | 214.65 | 119 | 143 |
| YAL017W | 25 | 27.83 | 34.43 | 67 | 92 |
| YDL040C | 29 | 77.41 | 89.84 | 96 | 125 |
| YMR315W | 35 | 337.83 | 379.29 | 178 | 196 |
| YHR158C | 37 | 26.66 | 38.24 | 48 | 85 |
| YHR159W | 38 | 12.74 | 42.8 | 11 | 11 |
| YML024W | 41 | 10,985.1 | 11,140.6 | 1,191 | 1,232 |
| YEL034C-A | 44 | 1,638.82 | 1,756.89 | 534 | 578 |
| YBL030C | 45 | 357.3 | 417.75 | 140 | 140 |
| YAR014C | 46 | 33.18 | 33.03 | 48 | 94 |
| YDR037W | 47 | 734.6 | 762.37 | 664 | 664 |
| YOL086C | 48 | 11,798 | 11,745.5 | 4,996 | 5,044 |
| YJR109C | 49 | 82.5 | 98.29 | 132 | 181 |
| YDR448W | 51 | 17.06 | 65.11 | 16 | 42 |
| YDR209C | 52 | 758.86 | 1,043.42 | 82 | 134 |
| YDR105C | 53 | 59.9842 | 104.932 | 51 | 104 |
| YDL130W | 54 | 6,880.78 | 7,315.38 | 596 | 596 |
| YBR191W | 55 | 6,798.73 | 6,972.36 | 752 | 807 |
| YDR083W | 55 | 93.1 | 122.52 | 61 | 116 |
| YBR110W | 58 | 107.46 | 159.57 | 66 | 124 |
| YBL092W | 59 | 10,264 | 10,540.1 | 1,530 | 1,589 |
| YCR012W | 61 | 3,729.34 | 3,796.95 | 3,705 | 3,766 |
| YOR378W | 63 | 6.59 | 56.45 | 2 | 2 |
| YML063W | 64 | 4,559.77 | 4,657.21 | 1,545 | 1,609 |
| YOR224C | 65 | 840.65 | 1,120.23 | 119 | 184 |
| YLR109W | 66 | 7,990.36 | 7,954.82 | 1,601 | 1,667 |
| YFR031C-A | 67 | 2,903.13 | 3,014.11 | 531 | 598 |
| YGR148C | 67 | 3,850.87 | 4,096.11 | 450 | 450 |
| YDL073W | 68 | 36.83 | 62.37 | 75 | 143 |
| YML059C | 69 | 5.8334 | 20.6487 | 19 | 19 |
| YPR089W | 70 | 31.3807 | 60.7936 | 58 | 128 |
| YDR226W | 71 | 1,914.74 | 2,064.52 | 544 | 579 |
| YPL104W | 71 | 23.56 | 65.08 | 27 | 98 |
| YOR122C | 72 | 3,148.49 | 3,553.19 | 386 | 458 |
| YHR102W | 73 | 14.09 | 14.03 | 33 | 106 |
| YDR023W | 74 | 524.92 | 587.48 | 409 | 409 |
| YBL055C | 75 | 97.12 | 170.68 | 45 | 45 |
| YBL091C | 76 | 204.38 | 277.81 | 125 | 125 |
| YJL090C | 77 | 17.48 | 55.69 | 25 | 25 |
| YJL188C | 78 | 5,103.93 | 5,614.29 | 802 | 880 |
| YGR106C | 79 | 728.12 | 724.89 | 277 | 356 |
| YJR072C | 79 | 200.13 | 285.26 | 138 | 138 |
| YOR123C | 81 | 110.42 | 180.59 | 93 | 174 |
| YPL154C | 82 | 398.23 | 480.465 | 203 | 203 |
| YPR074C | 83 | 404.86 | 449.98 | 384 | 384 |
| YFL039C | 84 | 2,343.94 | 2,427.94 | 1,093 | 1,177 |
| YDR050C | 85 | 9,632.29 | 9,751.83 | 3,113 | 3,198 |
| YMR142C | 85 | 4,407.12 | 4,387.52 | 1,041 | 1,126 |
| YDL191W | 86 | 7,255.86 | 7,223.59 | 272 | 272 |
| YGL102C | 87 | 3,688.69 | 3,785.85 | 1,686 | 1,773 |
| YHR193C | 88 | 2,017.73 | 2,008.75 | 547 | 547 |
| YKL145W | 89 | 360.33 | 436.22 | 227 | 316 |
| YMR012W | 90 | 95.84 | 121.20 | 191 | 281 |
| YOR298C-A | 92 | 1,066.95 | 1,439.52 | 190 | 282 |
| YGL012W | 93 | 297.35 | 375.37 | 169 | 169 |
| YDR212W | 94 | 263.12 | 328.14 | 219 | 313 |
| YBR048W | 95 | 3,710.64 | 4,062 | 353 | 448 |
| YBL052C | 96 | 28.92 | 74.09 | 47 | 47 |
| YAL041W | 97 | 50.87 | 50.65 | 65 | 65 |
| YAL038W | 98 | 3,610.93 | 3,613.65 | 4,517 | 4,555 |
| YPL220W | 98 | 5,828.52 | 6,028.35 | 312 | 410 |
| YKL060C | 99 | 17,531.1 | 17,570.5 | 9,999 | 9,999 |
| YPR145W | 99 | 563.698 | 629.111 | 526 | 526 |
| YOR369C | 100 | 18,149.4 | 18,068.7 | 3,126 | 3,226 |
| YER165W | 101 | 418.29 | 485.05 | 421 | 472 |
| YLR359W | 101 | 985.91 | 1,065.82 | 664 | 765 |
| YBR121C | 113 | 402.57 | 466.61 | 385 | 498 |
| YML009C | 123 | 691.233 | 2,465.9 | 29 | 91 |
| YNL178W | 146 | 8,261.72 | 8,516.73 | 2,245 | 2,300 |