A Semiautomatic Method to Achieve Independent and Intact Gene Ontology Slim (InitGO) and its Cytoscape Plugin Implementation

To conduct a systemic analysis of biological networks function distribution and function modules, we present a semiautomatic method to achieve independent and intact GO slim (InitGO) based on graph operations and GO hierarchy structure. Our method is packed into a user-friendly Cytoscape plugin named InitGO. The application of InitGO to yeast transcriptional factors regulatory network shows that the network has function modularity, offering evidence that our method is effective for defining function modules. InitGO plugin and source codes are available on request from the authors.