Identification potential biomarkers in pulmonary tuberculosis and latent infection based on bioinformatics analysis.
Identification potential biomarkers in pulmonary tuberculosis and latent infection based on bioinformatics analysis.
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DOI：
10.1186/s12879-016-1822-6
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发表时间：
2016-09-21
影响因子：
3.7
通讯作者：
Sun BJ
中科院分区：
文献类型：
--
作者：
Qin XB;Zhang WJ;Zou L;Huang PJ;Sun BJ
该研究旨在基于生物信息学分析，识别肺结核（TB）和结核潜伏感染的潜在生物标志物。 GSE57736的微阵列数据从Gene Expression Omnibus数据库下载。总共使用7份肺结核样本和8份潜伏感染样本来鉴定差异表达基因（DEG）。利用Cytoscape软件构建蛋白质-蛋白质相互作用(PPI)网络。然后进行基于网络的邻域评分分析来识别重要基因。此外，对鉴定出的重要基因进行功能富集分析、相关分析和Logistic回归分析。总共鉴定出 1084 个 DEG，其中包括 565 个下调基因和 519 个上调基因。 PPI网络由446个节点和768条边构成。下调基因 RIC8 鸟嘌呤核苷酸交换因子 A (RIC8A)、碱性亮氨酸拉链转录因子、ATF 样 (BATF) 和微管相关单加氧酶、钙调蛋白 LIM 结构域包含 1 (MICAL1) 和上调基因 ATPase、Na+/K+ 转运、α 4 多肽 (ATP1A4)、组蛋白簇 1、H3c (HIST1H3C)、组蛋白簇 2、 H3d (HIST2H3D)、组蛋白簇 1、H3e (HIST1H3E) 和酪氨酸激酶 2 (TYK2) 被选为基于网络的邻域评分分析中的重要基因。功能富集分析结果表明，这些重要的DEG主要富集在成骨细胞分化和三磷酸核苷生物合成过程的调节方面。基因对 RIC8A-ATP1A4、HIST1H3C-HIST2H3D、HIST1H3E-BATF 和 MICAL1-TYK2 经鉴定具有高度正相关性。此外，这些基因被选为逻辑回归分析中的显着特征基因。 RIC8A、ATP1A4、HIST1H3C、HIST2H3D、HIST1H3E、BATF、MICAL1和TYK2等基因可能是肺结核或结核潜伏感染的潜在生物标志物。
The study aimed to identify the potential biomarkers in pulmonary tuberculosis (TB) and TB latent infection based on bioinformatics analysis. The microarray data of GSE57736 were downloaded from Gene Expression Omnibus database. A total of 7 pulmonary TB and 8 latent infection samples were used to identify the differentially expressed genes (DEGs). The protein-protein interaction (PPI) network was constructed by Cytoscape software. Then network-based neighborhood scoring analysis was performed to identify the important genes. Furthermore, the functional enrichment analysis, correlation analysis and logistic regression analysis for the identified important genes were performed. A total of 1084 DEGs were identified, including 565 down- and 519 up-regulated genes. The PPI network was constructed with 446 nodes and 768 edges. Down-regulated genes RIC8 guanine nucleotide exchange factor A (RIC8A), basic leucine zipper transcription factor, ATF-like (BATF) and microtubule associated monooxygenase, calponin LIM domain containing 1 (MICAL1) and up-regulated genes ATPase, Na+/K+ transporting, alpha 4 polypeptide (ATP1A4), histone cluster 1, H3c (HIST1H3C), histone cluster 2, H3d (HIST2H3D), histone cluster 1, H3e (HIST1H3E) and tyrosine kinase 2 (TYK2) were selected as important genes in network-based neighborhood scoring analysis. The functional enrichment analysis results showed that these important DEGs were mainly enriched in regulation of osteoblast differentiation and nucleoside triphosphate biosynthetic process. The gene pairs RIC8A-ATP1A4, HIST1H3C-HIST2H3D, HIST1H3E-BATF and MICAL1-TYK2 were identified with high positive correlations. Besides, these genes were selected as significant feature genes in logistic regression analysis. The genes such as RIC8A, ATP1A4, HIST1H3C, HIST2H3D, HIST1H3E, BATF, MICAL1 and TYK2 may be potential biomarkers in pulmonary TB or TB latent infection.
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影响因子：
14.9
作者：
Keshava Prasad TS;Goel R;Kandasamy K;Keerthikumar S;Kumar S;Mathivanan S;Telikicherla D;Raju R;Shafreen B;Venugopal A;Balakrishnan L;Marimuthu A;Banerjee S;Somanathan DS;Sebastian A;Rani S;Ray S;Harrys Kishore CJ;Kanth S;Ahmed M;Kashyap MK;Mohmood R;Ramachandra YL;Krishna V;Rahiman BA;Mohan S;Ranganathan P;Ramabadran S;Chaerkady R;Pandey A
通讯作者：
Pandey A
影响因子：
64.5
作者：
Boshoff, HIM;Reed, MB;Mizrahi, V
通讯作者：
Mizrahi, V
影响因子：
9.2
作者：
Peterson, CL;Laniel, MA
通讯作者：
Laniel, MA
影响因子：
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作者：
Kanunfre, Kelly Aparecida;Munhoz Leite, Olavo Henrique;Ferreira, Antonio Walter
通讯作者：
Ferreira, Antonio Walter
影响因子：
3.6
作者：
Chowdhury, Imran Hussain;Ahmed, Albin Mostaque;Bahar, Bojlul
通讯作者：
Bahar, Bojlul