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Table 3 Comparison of microarray and real time PCR data

From: Transcriptional profiling of the LPS induced NF-κB response in macrophages

  Microarray Taqman
Gene 1 hr LPS 4 hr LPS 1 hr LPS 4 hr LPS
Chemokines and receptors
CCL3 5.744 2.200 1622 (± 322) 141 (± 27)
CCL3L1 5.708 2.603 56 (± 3) 4 (± 1)
CCL4 4.769 3.399 7047 (± 836) 2481 (± 714)
CCL8 * 1.859 NC 8 (± 2) 94 (± 38)
CCL22 NC 4.021 NC 135 (± 28)
CXCL1 * 1.272 NC 258 (± 41) 250 (± 21)
CXCL2 3.938 2.787 243 (± 85) 68 (± 13)
CXCL8 * NC 1.957 1016 (± 57) 491 (± 56)
CXCR4 NC -1.493 NC -4 (± 1)
Cytokines and receptors
IL-1β 4.649 4.289 3490 (± 254) 1891 (± 135)
IL-1RN * NC 1.830 4 6 (± 2)
PBEF 1.008 3.029 5 (± 2) 19 (± 1)
TNF-α 4.808 2.116 392 (± 55) 39 (± 4)
Stress
COX-2 3.673 1.333 166 (± 34) 29 (± 8)
SOD2 4.433 5.620 44 (± 7) 264 (± 37)
TXNIP -3.757 -1.638 -11 (± 2) -2 (± 1)
Apoptosis
cIAP2 * NC 1.151 19 (± 3) 112 (± 11)
GADD45β 1.212 1.323 7 (± 1) 8 (± 1)
PDCD4 NC -1.048 NC -7 (± 1)
PMAIP1 2.604 NC 7 (± 1) NC
TNFAIP3 2.905 2.526 104 (± 17) 44 (± 8)
Transcription
C-MYB NC -1.584 NC -5 (± 1)
TOP2α NC -1.561 NC -3
C-REL * NC 2.869 4 (± 1) 38 (± 3)
IκB-α 4.024 3.006 40 (± 4) 19 (± 2)
NFκB1 1.150 3.427 4 (± 1) 36 (± 2)
Cell cycle and Differentiation
BTG2 * 2.023 NC 116 (± 21) 32 (± 7)
BUB1β NC -1.244 NC -3
ID2 NC 1.299 NC 4 (± 1)
JARID1B π 2.675 4.061 NC NC
Growth
IGFBP3 * NC 4.182 43 (± 9) 1420 (± 167)
Adhesion     
ICAM1 * NC 1.188 6 70 (± 44)
Miscellaneous
HLA-DRα π NC 1.593 NC NC
SMYD5 π 3.699 2.417 NC NC
  1. Real time PCR results correspond to mean fold change normalised to GAPDH from 3 biological replicates and SEM is indicated. Genes where significantly different results between microarray and Taqman data was observed are indicated with an π. Genes which were originally scored as no change (NC) based on microarray data (at one time point) but where the increased sensitivity of Taqman revealed a change are indicated with an *. Note, any gene that showed a mean fold change between 2 and -2 was scored as NC in Taqman.