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Table 2 Comparison of the prediction profile with LIMMA analysis

From: mRNA expression profiles of primary high-grade central osteosarcoma are preserved in cell lines and xenografts

probeID symbol LIMMAlogFC CvsF LIMMAlogFC CvsO LIMMAlogFC FvsO LIMMAadjP pamrchondro-score pamrfibro-score pamrosteo-score
5910377 ACAN 2.42 2.24 -0.18 0.0000 0.9294 0 -0.0147
3390678 NFE2L3 -1.74 -0.02 1.71 0.0000 0 0.9184 0
1990523 COL9A1 3.49 3.01 -0.47 0.0000 0.6011 0 0
360553 SCRG1 4.55 3.51 -1.04 0.0001 0.4571 0 0
3310368 ID3 1.87 -0.29 -2.16 0.0003 0 -0.4053 0
10561 ITIH5L 0.68 0.65 -0.04 0.0001 0.295 0 0
5050110 MGC34761 0.93 0.83 -0.09 0.0002 0.2818 0 0
4780368 ACAN 1.34 1.19 -0.14 0.0004 0.2716 0 0
7150719 COL2A1 4.82 4.36 -0.47 0.0016 0.183 0 0
3830341 LYRM1 -1.23 -0.18 1.06 0.0007 0 0.1677 0
3990500 MATN4 1.96 1.69 -0.27 0.0012 0.151 0 0
4280370 POPDC3 -0.88 -0.08 0.80 0.0009 0 0.0909 0
6520487 UNQ830 4.10 2.90 -1.20 0.0016 0.0817 0 0
2850202 COL11A2 1.37 1.10 -0.27 0.0014 0.0735 0 0
4220452 C11ORF41 -0.89 -0.03 0.86 0.0011 0 0.0721 0
4560091 COL9A3 1.14 1.21 0.07 0.0018 0.0698 0 0
5890452 LOC652881 0.43 0.37 -0.06 0.0001 0.0666 0 0
3990259 PPP2R2B -1.00 0.10 1.10 0.0016 0 0.0603 0
5340392 MAN2A1 -1.42 -0.22 1.20 0.0018 0 0.0477 0
3360139 DLX5 1.84 -0.20 -2.04 0.0033 0 -0.0358 0
2630762 C14ORF78 -1.07 1.45 2.52 0.0011 0 0 -0.0307
3460037 UNQ1940 0.44 1.71 1.27 0.0018 0 0 -0.0219
6110722 COL2A1 1.22 1.44 0.22 0.0032 0.0087 0 0
6980164 ALPL 2.52 -0.67 -3.19 0.0038 0 -0.0036 0
  1. Comparison of the 24 genes obtained with pamr prediction with a factorial LIMMA analysis between the three different histological subtypes (CvsF: chondroblastic- vs fibroblastic, CvsO: chondroblastic- vs osteoblastic, FvsO: fibroblastic vs osteoblastic osteosarcoma), for which log fold changes (logFC) are shown for the different coefficients of the analysis. Note that the adjP shows the significance for the whole factorial LIMMA analysis, and does not reflect the adjPs per subanalysis.