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.