New analysis tools to support analysis and review have been implemented in the plant coexpression database "ATTED-II"

On September 27, 2024, Professor Takeshi Obayashi and his colleagues at the Graduate School of Information Sciences of Tohoku University have added new features to a plant gene coexpression database "ATTED-II".

Recent years, various plants have been studied with Next-generation sequencers. However, in "non-model plants" including practical plants such as crops and vegetables, the functions of many genes are still unknown, in contrast to "model plants" such as Arabidopsis thaliana which has been well studied in the laboratories. While various research approaches have been taken by researchers, one useful strategy is to examine groups of genes whose expression levels correlate and change under specific conditions or environments (genes in a coexpression relationship, referred as "coexpressed genes"). This is because coexpressed genes are often responsible for a series of some physiological functions together and are expected to be useful in understanding the functional cohesion and complex regulatory relationships of these genes. However, it is common for a single gene to be included in independent coexpression modules that function in different conditions and environments, then it was necessary to have a complicated analysis by specialists to understand properly.

ATTED-II has been developed since November 2004. It collects transcriptome data of major publicly available plant species, mainly model plants such as Arabidopsis, and analyzed in large scale. And it has been widely used as a database to search for coexpressed genes. However, even after identifying similarities in expression patterns among genes, it was not easy to identify the conditions and environmental factors involved in their coexpression, only with the functions in ATTED-II so far.

In this update, a new tool, "PC View," has been implemented to analyze the Principal Component (PC) of a coexpression relationship. PC View can be used to examine the conditions and environments under which two genes of interest are coexpressed. And newly implemented "CoexViewer"" allows users to view a correlation diagram of the expression patterns of the two genes of interest. These two tools help the users to better understand the physiological functions of the coexpressed genes and their regulatory relationships.

In addition to the above new features, information of wheat and barley has been added, enabling the viewing of coexpression information for a total of 11 plant species. And, in "NetworkDrawer", in which displays the correlation of coexpressed genes as a network, paralog information (genes with the same KO and KEGG Orthology) can be displayed. Furthermore, a link to Plant GARDEN (Genome And Resource Database Entry), a portal site that curates genome and marker information of various plant species, has been added from the gene information.

These new implementations to ATTED-II will also be presented the 1st Asia & Pacific Bioinformatics Joint Conference at Naha Cultural Arts Theater NAHArt on Oct 22 to 25, 2024.

ATTED-II is developed as a part of JST Database Integration Coordination Program (DICP), "Platform of gene network information for non-model plants (Principal Investigator: OBAYASHI Takeshi, Professor, Graduate School of Information Sciences, Tohoku University)".

< Plants included in ATTED-II (Total 11 species)>

• Arabidopsis
• Field mustard
• Soybean
• Medicago
• Rice
• Poplar
• Tomato
• Grape
• Maize
• Wheat (New)
• Barley (New)