Table 2

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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