|
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)
|
- 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
- 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
- bThe normalization methods in these references were not mentioned, but the most common method used for microarray data is Quantile normalization
