Regulatory gene networks and signaling pathways from primary osteoarthritis and Kashin-Beck disease, an endemic osteoarthritis, identified by three analysis software
Regulatory gene networks and signaling pathways from primary osteoarthritis and Kashin-Beck disease, an endemic osteoarthritis, identified by three analysis software
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DOI：
10.1016/j.gene.2012.10.006
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发表时间：
2013-01-01
期刊：
影响因子：
3.5
通讯作者：
Guo, Xiong
中科院分区：
文献类型：
--
作者：
Wang, Sen;Duan, Chen;Guo, Xiong
三个新的软件系统。 Ingenuity通路分析（IPA、TranscriptomeBrowser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，了解通路或网络分析软件具有优越的识别靶基因的功能，操作简单，可有效鉴别诊断和治疗KBD和OA。从KBD患者和OA患者的软骨样本中分离RNA。Agilent 44 K人类全基因组利用寡核苷酸微阵列检测差异表达基因。通过GeneHub分析，我们从IPA和TranscriptomeBrowser中鉴定出1个重要的经典通路和1个重要的网络，其中RAC2可能与KBD的发病机制关系最为密切。 IPA 和 TranscriptomeBrowser 适合进行通路分析，而 TranscriptomeBrowser 则适合进行网络分析。因此，从 IPA 和 TranscriptomeBrowser 分析中获得的重要基因可以更好地了解 KBD 发病机制的分子细节，并为骨软骨病的未来研究提供有用的通路和网络图谱 (C) 2012 Elsevier B.V. 保留所有权利。
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.