Table 3 Comparison of Published housekeeping genes with HKG Datasets Defined in This Study
Study | #samples | #HKG | #Tissues/cells studied | Technique | Normalization method | Housekeeping Gene Set Stratified by Normalization Methoda | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
TC (%) | UQ (%) | Median (%) | Quantile (%) | TMM (%) | DESeq (%) | TPM (%) | RPKM (%) | Lib_siz (%) | ||||||
(4) | 142 | 1789 | 79 | Microarray | NAb | 94 (5.25) | 91 (5.09) | 115 (6.43) | 111 (6.20) | 92 (5.14) | 89 (4.97) | 115 (6.43) | 76 (4.25) | 96 (5.37) |
(5) | 18 | 2403 | 18 | Microarray | NA | 110 (4.58) | 145 (6.03) | 158 (6.58) | 161 (6.70) | 132 (5.49) | 124 (5.16) | 158 (6.58) | 103 (4.29) | 133 (5.53) |
(6) | 42 | 1522 | 42 | Microarray | NA | 89 (5.84) | 112 (7.36) | 117 (7.69) | 115 (7.56) | 87 (5.72) | 88 (5.78) | 117 (7.69) | 80 (5.26) | 92 (6.04) |
(6) | NA | 15,050 | 32 | sequencing_MPSS | TPM | 516 (3.43) | 578 (3.84) | 566 (3.76) | 581 (3.86) | 550 (3.65) | 559 (3.71) | 566 (3.76) | 489 (3.25) | 559 (3.71) |
(7) | 2502 | 6909 | 18 | Sequencing_EST | NA | 398 (5.76) | 542 (7.84) | 533 (7.71) | 551 (7.98) | 463 (6.70) | 458 (6.63) | 533 (7.71) | 369 (5.34) | 471 (6.82) |
(8) | NA | 12,714 | 19 | sequencing_EST | NA | 583 (4.59) | 627 (4.93) | 642 (5.05) | 656 (5.16) | 610 (4.80) | 620 (4.88) | 642 (5.05) | 546 (4.29) | 628 (4.94) |
(9) | NA | 7896 | 32 | RNA-Seq | RPKM | 514 (6.51) | 628 (7.95) | 654 (8.28) | 656 (8.31) | 601 (7.61) | 594 (7.52) | 654 (8.28) | 441 (5.59) | 615 (7.79) |
(10) | 16 | 3804 | 16 | RNA-Seq | RPKM | 279 (7.33) | 361 (9.49) | 372 (9.78) | 379 (9.96) | 317 (8.33) | 315 (8.28) | 372 (9.78) | 212 (5.57) | 329 (8.64) |