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Table 4 Application of gene set analysis methods to diabetes data [3].

From: Microarray-based gene set analysis: a comparison of current methods

Top Pathways

NP

AP

GSEA-Category

  

   OXPHOS_HG-U133A_probes

0.071

1

   MAP00480_Glutathione_metabolism

0.091

1

   MAP00500_Starch_and_sucrose_metabolism

0.19

1

   MAP00252_Alanine_and_aspartate_metabolism

0.199

1

   GLUCO_HG-U133A_probes

0.202

1

   ......

...

...

GSEA-limma

  

   OXPHOS_HG-U133A_probes

<0.001

<0.001

   c18_U133_probes

0.004

0.88

   Human_mitoDB_6_2002_HG-U133A_probes

0.006

0.88

   Mitochondr_HG-U133A_probes

0.01

1

   MAP00190_Oxidative_phosphorylation

0.018

1

   ......

...

...

SAFE

  

   MAP00561_Glycerolipid_metabolism

0.011

1

   OXPHOS_HG-U133A_probes

0.021

1

   MAP00500_Starch_and_sucrose_metabolism

0.035

1

   MAP00240_Pyrimidine_metabolism

0.046

1

   GLUCO_HG-U133A_probes

0.049

1

   ......

...

...

GlobalTest

  

   MAP00252_Alanine_and_aspartate_meta...

0.106

1

   OXPHOS_HG-U133A_probes

0.123

1

   c23_U133_probes

0.14

1

   c25_U133_probes

0.144

1

   GLUCO_HG-U133A_probes

0.144

1

   ......

...

...

PCOT2

  

   c20_U133_probes

0.032

1

   OXPHOS_HG-U133A_probes

0.045

1

   MAP00190_Oxidative_phosphorylation

0.06

1

   FA_HG-U133A_probes

0.086

1

   c28_U133_probes

0.093

1

   ......

...

...

sigPathway

  

   c22_U133_probes

0.012

1

   c29_U133_probes

0.014

1

   OXPHOS_HG-U133A_probes

0.014

1

   c25_U133_probes

0.032

1

   MAP00252_Alanine_and_aspartate_metabolism

0.088

1

   ......

...

...

  1. 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.