Faculty of Public Health, Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
Gene. 2013 Jan 1;512(1):89-96. doi: 10.1016/j.gene.2012.10.006. Epub 2012 Oct 13.
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 44K 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.
三种新的软件系统，即 Ingenuity 通路分析（IPA）、转录组浏览器和 MetaCore，通过分析大骨节病（KBD）和原发性膝骨关节炎（OA）的软骨细胞微阵列数据进行比较，以了解哪种通路或网络分析软件具有优越的功能，能够识别目标基因，操作简便，对 KBD 和 OA 的鉴别诊断和治疗有效。从 KBD 患者和 OA 患者的软骨样本中分离出 RNA。使用 Agilent 44K 人类全基因组寡核苷酸微阵列检测差异表达基因。从 IPA 中，我们确定了一个显著的经典途径和两个显著的网络。从 GeneHub 分析中，我们得到了三个网络。从 TranscriptomeBrowser 分析中获得了一个显著的经典途径和一个显著的网络。从 IPA 中获得的 POSTN 和 LEF1，以及 IPA 和 TranscriptomeBrowser 共同鉴定的 RAC2，可能与 KBD 的发病机制最密切相关。根据我们的数据分析，IPA 和 TranscriptomeBrowser 适用于通路分析，而 TranscriptomeBrowser 适用于网络分析。从 IPA 和 TranscriptomeBrowser 分析中获得的显著基因可能更好地了解 KBD 发病机制中的分子细节，并为未来骨软骨病的研究提供有用的通路和网络图谱。
