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Table 4 The 23 GO MF annotations used in the proposed method

From: A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments

GO ID

GO MF Annotation

GO:0003674

Molecular function unknown

GO:0016740

Transferase activity

GO:0016787

Hydrolase activity

GO:0030528

Transcription regulator activity

GO:0005198

Structural molecule activity

GO:0005215

Transporter activity

GO:0005515

Protein binding

GO:0003677

DNA binding

GO:0003723

RNA binding

GO:0016491

Oxidoreductase activity

GO:0030234

Enzyme regulator activity

GO:0004672

Protein kinase activity

GO:0006874

Ligase activity

GO:0008233

Peptidase activity

GO:0016779

Nucleotidyltransferase activity

GO:0004871

Signal transducer activity

GO:0004386

Helicase activity

GO:0006874

Ligase activity

GO:0045182

Translation regulator activity

GO:0016853

Isomerase activity

GO:0004721

Phosphoprotein phosphatase activity

GO:0003774

Moter activity

Other

Other

  1. Molecular function unknown (GO: 0003674) from the GO slim annotation terms was included in the set of annotations for the calculation of LOI scores. In the yeast genome, there are nearly two thousand genes (about one third of the genome) that have the annotation 'molecular function' according to the SGD. From the set of interactions identified by 'Pathway Studio', nearly 15% involve a target or regulator of the annotation 'molecular function unknown'. Although a gene product's annotation may not yet characterized, it still can participate in biologically meaningful interactions for the analysis of microarray data. The consideration of the frequency at which a gene with undermined function is involved in an interacting partner with known annotations allows the LOI-method for the potential identification of useful biological interactions even when the function of one of the genes remains unknown. Ideally, as biological information of an organism's entire set of expressed proteins becomes known, the necessity of including an annotation of unknown molecular function will vanish.