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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
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CAT-GxD:对基因表达数据集的集中访问

Bryan Angelo P Roxas1, Jennifer Lising Roxas1, Jessica S Guo2

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研究人员现在可以很容易地使用新的中央访问基因表达数据集 (CAT-GxD) 搜索引擎分析细菌基因表达数据. 该工具简化了对Clostridioides difficile的多原子数据的访问,有助于假设生成和目标识别.

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细菌基因表达数据集.克洛斯特里迪奥伊德斯困难菌数据库数据库数据库是一个数据库.多个原子的多个原子.蛋白质组学是指蛋白质组学.文字转录学 (Transcriptomics) 是一个学科.

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科学领域:

  • 微生物学 微生物学
  • 生物信息学是一种生物信息学.
  • 基因组学就是基因组学.

背景情况:

  • 公共可用的细菌基因表达数据集广泛,但由于复杂性和专门的专业知识要求,难以访问和分析.
  • 对于统一和解释多原子数据集的工具有限,这阻碍了研究和假设测试.

研究的目的:

  • 开发一个集成的搜索引擎CAT-GxD,简化对公开可用的细菌基因表达数据的访问和分析.
  • 为了促进使用多omics数据集进行比较和假设驱动的研究.

主要方法:

  • 使用R-shiny开发了使用基因表达数据集 (CAT-GxD) 的集中访问搜索引擎.
  • 手动策划和标准化74个转录组学和蛋白质组学数据集Clostridioides difficile来自GEO和ProteomeXchange.
  • 整合不同的数据集以实现统一的访问和分析.

主要成果:

  • CAT-GxD成功地整合了Clostridioides difficile的转录组学和蛋白组学数据.
  • 该搜索引擎在各种条件下提供可定制的基因表达数据可视化.
  • 在分析C. difficile中RpoN调节的证明有用性,包括对酸盐和脱氧酸盐的反应.

结论:

  • CAT-GxD简化了对C. difficile的多原子数据分析,减少了复杂性和时间.
  • 该工具促进了新的假设生成和抗感染标的识别.
  • CAT-GxD可以适应各种生物和数据分析范式.