Table 2 |
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|
Comparison of the prediction profile with LIMMA analysis |
||||||||
|
probeID |
symbol |
LIMMA logFC CvsF |
LIMMA logFC CvsO |
LIMMA logFC FvsO |
LIMMA adjP |
pamr chondro-score |
pamr fibro-score |
pamr osteo-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 |
|
|
||||||||
|
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. |
||||||||
|
Kuijjer et al. BMC Medical Genomics 2011 4:66 doi:10.1186/1755-8794-4-66 |
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