GSVAscore reveals molecular signatures from transcriptomes for biomaterials comparison
GSVAscore reveals molecular signatures from transcriptomes for biomaterials comparison
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DOI：
10.1002/jbm.a.37090
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发表时间：
2020-09-09
影响因子：
4.9
通讯作者：
Zambuzzi, Willian F.
中科院分区：
文献类型：
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作者：
Ferreira, Marcel R.;Santos, Gerson A.;Zambuzzi, Willian F.
采用两种计算机模拟方法，从转录组数据库中揭示无机羟基磷灰石和β-TCP材料的分子特征，以比较生物材料。为了测试这种新的方法，我们选择了阵列E-MTAB-7219，其中包含的成骨细胞系的转录谱接种到15个不同的生物材料长达48小时。该方法的扩展潜力进行了测试，从定制的签名建设。我们首次提出了一种方法，通过基因集变异分析（GSVA）评分，使用细胞的转录组谱来比较不同生物材料的性能。为了测试这种方法，我们实现了两种基于MSigDB集合的方法，使用了除Hallmark集合（用于第二种方法）之外的所有集合和子集合。该分析的结果提供了基于细胞转录景观的生物材料分组的初步理解。使用GSVA评分的比较结合了各种努力，并扩大了使用转录组谱比较生物材料的潜力。总之，我们的研究结果提供了一个更好的理解不同的生物材料的比较，并提出了新的方法学应用于新的生物材料的前景。
Two in silico methodologies were implemented to reveal the molecular signatures of inorganic hydroxyapatite and beta-TCP materials from a transcriptome database to compare biomaterials. To test this new methodology, we choose the array E-MTAB-7219, which contains the transcription profile of osteoblastic cell line seeded onto 15 different biomaterials up to 48 hr. The expansive potential of the methodology was tested from the construction of customized signatures. We present, for the first time, a methodology to compare the performance of different biomaterials using the transcriptome profile of the cell through the Gene set variation analysis (GSVA) score. To test this methodology, we implemented two methods based on MSigDB collections, using all the collections and sub-collections except the Hallmark collection, which was used in the second method. The result of this analysis provided an initial understanding of biomaterial grouping based on the cell transcriptional landscape. The comparison using GSVA score combined efforts and expand the potential to compare biomaterials using transcriptome profile. Altogether, our results provide a better understanding of the comparison of different biomaterials and suggest a possibility of the new methodology be applied to the prospection of new biomaterials.