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Table 3 Comparison of Published housekeeping genes with HKG Datasets Defined in This Study

From: Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue

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)
  1. Abbreviations: EST expressed sequence tags, HKG housekeeping genes, MPSS Massively parallel signature sequencing, ABMR antibody mediated rejection, DE differentially expressed, TCMR T-cell mediated rejection, PVAN polyomavirus nephropathy, NA not available; for other abbreviations, see legend to Table 1
  2. aThe total number (%) of overlapping genes with the specified datasets is enumerated. Percentage calculations are based on the total number of HKG in column 3
  3. bThe normalization methods in these references were not mentioned, but the most common method used for microarray data is Quantile normalization