Identification of genes and pathways in the synovia of women with osteoarthritis by bioinformatics analysis.
Identification of genes and pathways in the synovia of women with osteoarthritis by bioinformatics analysis.
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DOI：
10.3892/mmr.2018.8429
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发表时间：
2018-03
影响因子：
3.4
通讯作者：
Liu J
中科院分区：
文献类型：
--
作者：
Mi B;Liu G;Zhou W;Lv H;Liu Y;Liu J
骨关节炎（OA）在女性患者中的患病率较高，性别可能是影响OA进展的关键因素。本研究的目的是确定女性OA患者滑膜中的遗传标记，并阐明潜在的相关分子机制。从Gene Expression Omnibus数据库获得GSE 55457和GSE 55584数据集的基因表达谱。两个正常女性个体的滑膜数据（GSM1337306和GSM1337310）和来自受OA影响的女性患者的两种滑膜从数据集GSE 55457中获得GSM1337327和GSM1337330，并且从受OA影响的女性患者的三种滑膜中获得GSM1337327和GSM1337330。（GSM 1339628、GSM 1339629和GSM 1339632）从数据集GSE 55584获得。用Morpheus软件对差异表达基因进行鉴定。利用Cytoscape软件构建了DEG的蛋白质相互作用（PPI）网络。随后，通过使用CIMGO进行PPI网络的顶部模块的基因本体（GO）功能和京都基因和基因组百科全书（KEGG）途径富集分析。与正常人相比，OA患者滑膜中共鉴定出377个DEG，包括164个上调和213个下调基因。居前10位的枢纽基因依次为泛素（UB）C、核糖体蛋白（RP）L23A、哺乳动物雷帕霉素靶蛋白、热休克蛋白90 α家族A类成员1、RPS28、RPL37A、RPS24、RPS4X、RPS18和UBB。GO分析的结果表明，包含在PPI的顶部模块的DEG主要集中在术语“核转录的mRNA分解代谢过程”，“无义介导的衰变”和“细胞质翻译和核糖体小亚基生物合成”。KEGG途径分析表明，前一个模块中的DEG主要富集在“核糖体”途径。目前的研究提供了一个系统的，分子水平的了解滑膜的退化，在发展中的OA女性患者。与滑膜相关的枢纽基因和分子可用作女性OA患者治疗OA的生物标志物和治疗靶点。
Osteoarthritis (OA) has a high prevalence in female patients and sex may be a key factor affecting the progression of OA. The aim of the present study was to identify genetic signatures in the synovial membranes of female patients with OA and to elucidate the potential associated molecular mechanisms. The gene expression profiles of the GSE55457 and GSE55584 datasets were obtained from the Gene Expression Omnibus database. Data of two synovial membranes from normal female individuals (GSM1337306 and GSM1337310) and two synovial membranes from female patients affected by OA (GSM1337327 and GSM1337330) were obtained from the dataset GSE55457, and those of three synovial membranes from female patients affected by OA (GSM1339628, GSM1339629 and GSM1339632) were obtained from the dataset GSE55584. Differentially expressed genes (DEGs) were identified by using Morpheus software. Protein-protein interaction (PPI) networks of the DEGs were constructed by using Cytoscape software. Subsequently, Gene Ontology (GO) function and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses of the top module of the PPI network were performed by using ClueGo. A total of 377 DEGs were identified in the synovial membranes of OA patients compared with those of normal individuals, including 164 upregulated and 213 downregulated genes. The top 10 hub genes were ubiquitin (UB)C, ribosomal protein (RP) L23A, mammalian target of rapamycin, heat shock protein 90 α family class A member 1, RPS28, RPL37A, RPS24, RPS4X, RPS18 and UBB. The results of the GO analysis indicated that the DEGs included in the top module of the PPI were mainly enriched in the terms ‘nuclear-transcribed mRNA catabolic process’, ‘nonsense mediated decay’, and ‘cytoplasmic translation and ribosomal small subunit biogenesis’. KEGG pathway analysis indicated that the DEGs included in the top one module were mainly enriched in the ‘ribosome’ pathway. The present study provides a systematic, molecular-level understanding of the degeneration of the synovial membrane in the progression of OA in female patients. The hub genes and molecules associated with the synovial membrane may be used as biomarkers and therapeutic targets for the treatment of OA in female patients with OA.
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影响因子：
2.3
作者：
Prieto-Potin I;Largo R;Roman-Blas JA;Herrero-Beaumont G;Walsh DA
通讯作者：
Walsh DA
影响因子：
4.1
作者：
Takano S;Uchida K;Miyagi M;Inoue G;Fujimaki H;Aikawa J;Iwase D;Minatani A;Iwabuchi K;Takaso M
通讯作者：
Takaso M
影响因子：
7
作者：
Deligne, C.;Casulli, S.;Houard, X.
通讯作者：
Houard, X.
影响因子：
9.8
作者：
Doherty, Leana;Sheen, Mee Rie;Gazda, Hanna T.
通讯作者：
Gazda, Hanna T.
DOI：
10.1093/bioinformatics/btp101
发表时间：
2009-04-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Bindea G;Mlecnik B;Hackl H;Charoentong P;Tosolini M;Kirilovsky A;Fridman WH;Pagès F;Trajanoski Z;Galon J
通讯作者：
Galon J