Skip to main content

Table 1 Significant functional classes across a case-control study of diabetes.

From: From genes to functional classes in the study of biological systems

  

Repository

Method

Healthy vs diabetic

Functional class

GO

KEGG

Swissprot keyword

Defined in GSEA

FatiScan

GSEA

PAGE

Tian et al.

Up-regulated

Oxidative phosphorylation

•

•

 

•

yes

yes

yes

yes

 

ATP synthesis

 

•

  

yes

-

-

-

 

Ribosome

 

•

  

yes

-

-

-

 

Ubiquinone

  

•

 

yes

-

-

-

 

Ribosomal protein

  

•

 

yes

-

-

-

 

Ribonucleoprotein

  

•

 

yes

-

-

-

 

Mitochondrion

•

 

•

•

yes

yes

yes

yes

 

Transit peptide

  

•

 

yes

-

-

-

 

Nucleotide biosynthesis

•

  

•

yes

yes

yes

yes

 

NADH dehidrogenase (ubiquinone) activity

•

   

yes

-

-

-

 

Nuclease activity

•

   

yes

-

-

-

Dow-regulated

Insulin signalling pathway

 

•

  

yes

-

-

-

  1. Different functional classes, making reference to distinct functional terms, found as over-represented at the extremes of the list of genes ordered by differential expression between healthy controls versus diabetic cases (see text) by distinct threshold-free methods. Some of the functional classes refer to similar functional concepts and contain essentially the same genes, but have been defined in different repositories (GO, KEGG, etc.) FatiScan uses functional classes defined through GO, KEGG and Swissprot keywords (among other), while GSEA, PAGE and Tian et al. use the functional classes defined in GSEA [17].