Three　new　software　systems.　Ingenuity　pathway　analysis(IPA,　TranscriptomeBrowser　and　MetaCore,　were　compared　by　analyzing　chondrocyte　microarray　data　of　Kashin-Beck　disease　(KBD)　and　primary　knee　osteoarthritis(OA)　to　understand　the　pathway　or　network　analysis　software　which　has　a　superior,　function　to　identify　target　genes　with　easy　operation　and　effective　for　differential　diagnosis　and　treatment　of　KBD　and　OA.　RNA　was　isolated　from　cartilage　samples　taken　from　KBD　patients　and　OA　ones.　Agilent　44　K　human　whole　genome　oligonucleotide　microarrays　were　used　to　detect　differentially　expressed　genes.　From　IPA,　we　identified　one　significant　canonical　pathway　and　two　significant　networks.　From　GeneHub　analysis,　we　got　three　networks.　One　significant　canonical　pathway　and　one　significant　network　were　obtained　from　TranscriptomeBrowser　analysis.　POSTN　and　LEF1　which　were　got　from　IPA,　RAC2　which　was　identified　by　both　of　the　IPA　and　TranscriptomeBrowser　may　be　most　closely　related　to　the　etiopathogenesis　of　KBD.　According　to　our　data　analysis,　IPA　and　TranscriptomeBrowser　are　suitable　for　pathway　analysis,　while,　TranscriptomeBrowser　is　suitable　for　network　analysis.　The　significant　genes　obtained　from　IPA　and　TranscriptomeBrowser　analysis　may　thus　provide　a　better　understanding　of　the　molecular　details　in　the　pathogenesis　of　KBD　and　also　provide　useful　pathways　and　network　maps　for　future　research　in　osteochondrosis.　(C)　2012　Elsevier　B.V.　All　rights　reserved.