Wang Sen, Wang Weizhuo, Zhao Junjie, Zhang Feng, He Shulan, Guo Xiong
Int J Data Min Bioinform. 2015;12(1):100-14. doi: 10.1504/ijdmb.2015.068963.
In order to screen the more effective software for the pathway and network analysis of Kashin-Beck disease, gene microarrays, TranscriptomeBrowser, MetaCore and GeneMANIA were used for analysis. Three significant chondrocytic pathways and one network were screened by TranscriptomeBrowser; one significant pathway and one network were identified by MetaCore. BAX, APAF1, CASP6, BCL2, VEGF, SOCS3, BAK, TGFBI, TNFAIP6, TNFRSF11B and THBS1 were significant genes associated with the biological function of chondrocyte or cartilage involved in the TranscriptomeBrowser or MetaCore results. The interactions between the significant genes and their adjacent genes were searched and classified in GeneMANIA. In pathway analysis results, TranscriptomeBrowser is superior to get the interaction of pathway and co-expression compared with MetaCore; MetaCore is superior to get the interaction of physical interaction compared with TranscriptomeBrowser. In network analysis results, TranscriptomeBrowser contains more interaction message of co-localisation, MetaCore contains, more interaction message of co-expression.
为筛选出用于大骨节病通路和网络分析的更有效软件，使用基因芯片、转录组浏览器、MetaCore和基因共表达网络分析工具（GeneMANIA）进行分析。转录组浏览器筛选出三条显著的软骨细胞通路和一个网络；MetaCore鉴定出一条显著通路和一个网络。BAX、凋亡蛋白酶激活因子1（APAF1）、半胱天冬酶6（CASP6）、B细胞淋巴瘤/白血病-2（BCL2）、血管内皮生长因子（VEGF）、细胞因子信号转导抑制因子3（SOCS3）、BAK、转化生长因子β诱导蛋白（TGFBI）、肿瘤坏死因子α诱导蛋白6（TNFAIP6）、肿瘤坏死因子受体超家族成员11B（TNFRSF11B）和血小板反应蛋白1（THBS1）是与转录组浏览器或MetaCore结果中软骨细胞或软骨生物学功能相关的显著基因。在基因共表达网络分析工具中搜索并分类显著基因与其相邻基因之间的相互作用。在通路分析结果中，与MetaCore相比，转录组浏览器在获取通路相互作用和共表达方面更具优势；与转录组浏览器相比，MetaCore在获取物理相互作用方面更具优势。在网络分析结果中，转录组浏览器包含更多共定位的相互作用信息，MetaCore包含更多共表达的相互作用信息。
