Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

DEG identification and PageMan analysis

YY YanLing Yin
TY TianHui Yang
SL Shuang Li
XL Xiaoning Li
WW Wei Wang
SF ShuGao Fan
request Request a Protocol
ask Ask a question
Favorite

DEGs in the transcriptome data were identified through the utilization of the DESeq2 package (v1.22.1) within the R programming environment. Raw read counts were used as input data for the analysis. DEGs were identified using criteria where the absolute value of log2 (fold change (FC)) ≥ 1, and the false discovery rate (FDR) < 0.05.

Enrichment analysis of the DEGs was performed using the PageMan software (v3.0.0), which is a commonly used tool for functional analysis of large-scale omics data in plants. The log2 (FC) of NaCl vs. CK and that of NaCl+MeJA vs. CK were input into PageMan, and the significantly enriched BINs were identified using the Wilcoxon statistical test with default parameters provided by PageMan.

Copyright and License information:  ©2023 Yin, Yang, Li, Li, Wang and Fan
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A