Table 1

Differentially expressed gene groups between the PSKO and CNT mice regardless of age or brain region.
#
 NAME
 SIZE
 ES
 NES
 p-val
 q-val
1
 GABAPATHWAY
 11
 0.68
 1.59
 0.046748
 0.147418
2
 AGPCRPATHWAY
 10
 0.67
 1.45
 0.019068
 0.243600
3
 RAC1PATHWAY
 21
 -0.59
 -1.30
 0.020121
 0.418927
4
 D4GDIPATHWAY
 10
 -0.68
 -1.31
 0.043478
 0.397110
5
 ALKPATHWAY
 32
 -0.55
 -1.34
 0.014085
 0.298667
6
 NTHIPATHWAY
 19
 -0.61
 -1.35
 0.040936
 0.290866
7
 TGFBPATHWAY
 13
 -0.67
 -1.42
 0.010142
 0.163844
8
 MCALPAINPATHWAY
 22
 -0.53
 -1.44
 0.005848
 0.179323
9
 INTRINSICPATHWAY
 20
 -0.58
 -1.45
 0.020534
 0.177983
10
 LAIRPATHWAY
 10
 -0.67
 -1.45
 0.046185
 0.198237
11
 VITCBPATHWAY
 10
 -0.51
 -1.45
 0.038776
 0.228195
12
 TOB1PATHWAY
 14
 -0.73
 -1.63
 0.004082
 0.087297
13
 EXTRINSICPATHWAY
 12
 -0.71
 -1.69
 0.014614
 0.082402
14
 NKCELLSPATHWAY
 15
 -0.50
 -1.70
 0.025490
 0.138997

The whole dataset was subjected to pathway analysis with BioCarta using GSEA. Significantly enriched pathways are presented in either direction (positive NES – enriched in CNT; negative NES – enriched in PSKO). Abbreviations: SIZE- number of non-redundant probes in a pathway; ES – enrichment score; NES – normalized enrichment score; p-val – groupwise p value; q-val – groupwise false discovery ratio estimate. Note that only 2 pathways were enriched in the CNT mice (GABA and AGPCR), while the PSKO mice samples were enriched in 12 pathways.

Mirnics et al. Molecular Neurodegeneration 2008 3:14   doi:10.1186/1750-1326-3-14