Plant epitranscriptome analysis

PEA: an Integrated R Toolkit for Plant Epitranscriptome Analysis

**MOTIVATION**: The epitranscriptome, also known as chemical modifications of RNA (CMRs), is a newly discovered layer of gene regulation, the biological importance of which emerged through analysis of only a small fraction of CMRs detected by …

Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development

In angiosperms, the endosperm provides nutrients for embryogenesis and seed germination and is the primary tissue where gene imprinting occurs. To identify the imprintome of early developing maize (Zea mays) endosperm, we performed high-throughput …

Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis

One of the computational challenges in plant systems biology is to accurately infer transcriptional regulation relationships based on correlation analyses of gene expression patterns. Despite several correlation methods that are applied in biology to …


Gini-based transcriptiome analysis