ATTED-II v11: A Plant Gene Coexpression Database Using a Sample Balancing Technique by Subagging of Principal...

Area of Science:

• Plant biology
• Bioinformatics
• Genomics

Background:

• Publicly available gene expression data (RNAseq, microarray) are crucial for building coexpression databases.
• Managing sampling bias in public data is a key challenge for condition-independent coexpression analysis.
• ATTED-II is a gene coexpression database for nine plant species.

Purpose of the Study:

• To report ATTED-II version 11, incorporating improved methods for managing sampling bias.
• To enhance the accuracy and utility of plant gene coexpression data.
• To facilitate interspecies comparative studies and integrated analyses.

Main Methods:

• Developed a coexpression calculation methodology using principal component analysis (PCA) and ensemble calculation to balance samples.
• Reduced noise by omitting principal components with low contribution rates.
• Integrated RNAseq- and microarray-based coexpression data for species-representative information.

Main Results:

• Implemented a novel method to balance samples, reducing noise and accounting for diverse sample conditions.
• Provided standardized z-scores for coexpression data, enabling integrated analysis across different data sources.
• Enhanced interspecies comparison of gene coexpression patterns.

Conclusions:

• ATTED-II version 11 offers a more powerful and valuable resource for plant biology research.
• The improved methodology enhances the reliability of coexpression data.
• Facilitates cross-species gene coexpression studies and integrated analysis of diverse datasets.