As tremendous genomic data avalanches, exploring biological mechanism by data analysis and theory methods has become important for theoretical biology research. This method is significant for the study of complex gene functions and gene networks. Bowers used higher order logic relationships to decipher protein network organization, which is a systemic method called logic analysis of phylogenetic profiles (LAPP). LAPP is a data modeling and different from traditional computational methods. This computational approach identifies logic relationships of the elements (or components) in complex networks through the logic analysis of their expression data. The method can be used to infer functional relationships of two associated proteins to one another. It is important for discovering the new function mechanism of the protein. The clusters of orthologous groups (COGs) involved in a gene network usually are large groups and therefore LAPP is also an approach for complex gene logic networks. After the establishment of the gene logic network, it is convenient for the regulation of gene through the network. The method can used in many fields, such as species evolution, oncologic diagnosis and so on. LAPP was systematically described and analyzed and recent developments in methodologies and applications were highlighted. Some opinions of them were also given.