We propose an iterative ranking-based method called C r o G O2 to measure the cross-categories GO term similarities by incorporating level information of GO terms with both direct and indirect interactions in the gene co-function network.


 The evaluation test shows that C r o G O2 performs better than the existing methods. 
C r o G O2
Identifying term relations cross different gene ontology categories.BACKGROUND
 The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function.  GO includes three independent categories: molecular function, biological process and cellular component.  For better biological reasoning, identifying the biological relationships between terms in different categories are important.  However, the existing measurements to calculate similarity between terms in different categories are either developed by using the GO data only or only take part of combined gene co-function network information.


 We propose an iterative ranking-based method called C r o G O2 to measure the cross-categories GO term similarities by incorporating level information of GO terms with both direct and indirect interactions in the gene co-function network.


 The evaluation test shows that C r o G O2 performs better than the existing methods.  Given a gene set, the related terms identified by using the association network have overlap with the related terms identified by GO enrichment analysis.
GO