Table 5 |
||
|
Application of gene set analysis methods to leukemia data [22]. |
||
|
Top Pathways |
NP |
AP |
|
|
||
|
GSEA-Category |
||
|
Glycolysis/Gluconeogenesis |
<5e-05 |
<5e-05 |
|
Focal adhesion |
<5e-05 |
<5e-05 |
|
Tight junction |
<5e-05 |
<5e-05 |
|
Leukocyte transendothelial migration |
<5e-05 |
<5e-05 |
|
Regulation of actin cytoskeleton |
<5e-05 |
<5e-05 |
|
...... |
... |
... |
|
|
||
|
GSEA-limma |
||
|
Hematopoietic cell lineage |
<5e-05 |
0.034 |
|
B cell receptor signaling pathway |
<5e-05 |
0.034 |
|
Glutathione metabolism |
0.017 |
1 |
|
Glycolysis/Gluconeogenesis |
0.025 |
1 |
|
Natural killer cell mediated cytotoxicity |
0.028 |
1 |
|
...... |
... |
... |
|
|
||
|
SAFE |
||
|
Natural killer cell mediated cytotoxicity |
0.0052 |
1 |
|
Glycolysis/Gluconeogenesis |
0.00835 |
1 |
|
Galactose metabolism |
0.0128 |
1 |
|
Pyrimidine metabolism |
0.0333 |
1 |
|
Cell cycle |
0.0353 |
1 |
|
...... |
... |
... |
|
|
||
|
GlobalTest |
||
|
Toll-like receptor signaling pathway |
<5e-05 |
<5e-05 |
|
Jak-STAT signaling pathway |
<5e-05 |
<5e-05 |
|
Focal adhesion |
<5e-05 |
<5e-05 |
|
Tight junction |
<5e-05 |
<5e-05 |
|
Leukocyte transendothelial migration |
<5e-05 |
<5e-05 |
|
...... |
... |
... |
|
|
||
|
PCOT2 |
||
|
Jak-STAT signaling pathway |
<5e-05 |
0.001 |
|
Glycolysis Gluconeogenesis |
<5e-05 |
0.001 |
|
Focal adhesion |
<5e-05 |
0.001 |
|
Tight junction |
<5e-05 |
0.001 |
|
Hematopoietic cell lineage |
<5e-05 |
0.001 |
|
...... |
... |
... |
|
|
||
|
sigPathway |
||
|
Arachidonic acid metabolism |
<5e-05 |
0.001 |
|
Metabolism of xenobiotics by cytochrome P450 |
<5e-05 |
0.004 |
|
Glutathione metabolism |
<5e-05 |
0.009 |
|
Cell cycle |
0.0001 |
0.016 |
|
Starch and sucrose metabolism |
0.0002 |
0.023 |
|
...... |
... |
... |
|
|
||
|
Top five altered gene sets determined by each of the six analysis methods. NP indicates the nominal p-values and AP indicates the FDR adjusted p-values. |
||
|
Song and Black BMC Bioinformatics 2008 9:502 doi:10.1186/1471-2105-9-502 |
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