RNA-Seq co-expression analysis and candidate selection

YL Yuping Li
YQ Yuan Qiu
XX Xin Xu
ML Ming Luo
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Using RNA-Seq data from different tissues of two S. rebaudiana varieties, we identified enzyme-coding structural genes involved in RA biosynthesis, including ent-KS, ent-KO, ent-KAH, UGT74G1, UGT85C2, UGT91D2, and UGT76G1. These structural genes were used as bait to screen bHLH transcription factors that potentially regulate RA biosynthesis. Co-expression relationships between structural genes and SrbHLHs were estimated using Pearson correlation analysis. We filtered a set of co-expressed SrbHLHs genes using a Pearson coefficient threshold of 0.95 and p < 0.05. The OmicShare tools, a free online platform for data analysis (https://www.omicshare.com/tools), were applied to construct the structural-SrbHLH gene network.

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