Shannon entropy as a metric for conditional gene expression in Neurospora crassa.
Shannon entropy as a metric for conditional gene expression in Neurospora crassa.
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DOI：
10.1093/g3journal/jkab055
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发表时间：
2021-04-15
期刊：
影响因子：
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通讯作者：
Lewis ZA
中科院分区：
文献类型：
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作者：
Ameri AJ;Lewis ZA
粗糙脉孢菌作为分子生物学和遗传学的重要模式生物已有60多年的历史。粗糙脉孢菌具有复杂的生命周期，具有超过28种不同的细胞类型，并且能够对许多环境条件（包括营养物可用性、温度和光照）进行转录响应。为了量化N. crassa基因表达，我们分析了来自97种条件的公开表达数据，并计算了脉孢菌约11，000个基因的香农熵值。熵值可用于估计单个基因在一系列条件下表达的变异性，并用于将单个基因分类为组成型或条件特异性。香农熵以前曾被用来衡量多细胞植物或动物基因的组织特异性程度。我们在这里使用这个指标来测量微生物中可变的基因表达，并将此信息作为N。crassa研究社区。最后，我们证明了这种方法的实用性，通过使用熵值来识别在广泛的条件下组成型表达的基因，并识别在性发育过程中被激活的基因。
Neurospora crassa has been an important model organism for molecular biology and genetics for over 60 years. Neurospora crassa has a complex life cycle, with over 28 distinct cell types and is capable of transcriptional responses to many environmental conditions including nutrient availability, temperature, and light. To quantify variation in N. crassa gene expression, we analyzed public expression data from 97 conditions and calculated the Shannon Entropy value for Neurospora’s approximately 11,000 genes. Entropy values can be used to estimate the variability in expression for a single gene over a range of conditions and be used to classify individual genes as constitutive or condition-specific. Shannon entropy has previously been used measure the degree of tissue specificity of multicellular plant or animal genes. We use this metric here to measure variable gene expression in a microbe and provide this information as a resource for the N. crassa research community. Finally, we demonstrate the utility of this approach by using entropy values to identify genes with constitutive expression across a wide range of conditions and to identify genes that are activated exclusively during sexual development.