Table 1

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

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

-

-

-


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].

Al-Shahrour et al. BMC Bioinformatics 2007 8:114   doi:10.1186/1471-2105-8-114

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