Nowadays high-throughput omics technologies are routinely used in biological research. From the omics data, researchers can easily get two gene lists (e.g. stress-induced genes vs. stress-repressed genes) related to their biological question. The next step would be to apply enrichment analysis tools to identify distinct functional/regulatory features between these two gene lists for further investigation. Although various enrichment analysis tools are already available, two challenges remain to be addressed. First, most existing tools are designed to analyze only one gene list, so they cannot directly compare two gene lists. Second, almost all existing tools focus on identifying the enriched qualitative features (e.g. gene ontology [GO] terms, pathways, domains, etc.). Many quantitative features (e.g. number of mRNA isoforms of a gene, mRNA half-life, protein half-life, transcriptional plasticity, translational efficiency, etc.) are available in the yeast, but no existing tools provide analyses on these quantitative features. To address these two challenges, here we present Yeast Quantitative Features Comparator (YQFC) that can directly compare various quantitative features between two yeast gene lists. In YQFC, we comprehensively collected and processed 85 quantitative features from the yeast literature and yeast databases. For each quantitative feature, YQFC provides three statistical tests (t-test, U test and KS test) to test whether this quantitative feature is statistically different between the two input yeast gene lists. The distinct quantitative features identified by YQFC may help researchers to study the underlying molecular mechanisms that differentiate the two input yeast gene lists. We believe that YQFC is a useful tool to expedite the biological research that uses high-throughput omics technologies.

中文翻译：

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YQFC：一种比较两个酵母基因列表之间定量生物学特征的网络工具

如今，高通量组学技术已被广泛用于生物学研究。从组学数据中，研究人员可以轻松获得与他们的生物学问题相关的两个基因列表（例如压力诱导基因与压力抑制基因）。下一步将是应用富集分析工具来识别这两个基因列表之间不同的功能/调节特征，以进行进一步研究。尽管各种富集分析工具已经可用，但仍有两个挑战需要解决。首先，大多数现有工具仅设计用于分析一个基因列表，因此它们不能直接比较两个基因列表。其次，几乎所有现有工具都专注于识别丰富的定性特征（例如基因本体 [GO] 术语、途径、域等）。许多定量特征（例如基因的 mRNA 同种型的数量，mRNA 半衰期、蛋白质半衰期、转录可塑性、翻译效率等）在酵母中可用，但没有现有工具提供对这些定量特征的分析。为了解决这两个挑战，我们在这里提出了酵母定量特征比较器 (YQFC)，它可以直接比较两个酵母基因列表之间的各种定量特征。在YQFC中，我们从酵母文献和酵母数据库中综合收集和处理了85个定量特征。对于每个定量特征，YQFC 提供了三个统计检验（t 检验、U 检验和 KS 检验）来检验该定量特征在两个输入酵母基因列表之间是否存在统计差异。YQFC 确定的独特定量特征可能有助于研究人员研究区分两种输入酵母基因列表的潜在分子机制。我们相信 YQFC 是一种有用的工具，可以加快使用高通量组学技术的生物学研究。