Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants

by Sourabh Palande, Joshua A. M. Kaste, Miles D. Roberts, Kenia Segura Ab á, Carly Claucherty, Jamell Dacon, Rei Doko, Thilani B. Jayakody, Hannah R. Jeffery, Nathan Kelly, Andriana Manousidaki, Hannah M. Parks, Emily M. Roggenkamp, Ally M. Schumacher, Jiaxin Yang, Sarah Percival, Jeremy Pardo, Aman Y. Husbands, Arjun Krishnan, Beronda L Montgomery, Elizabeth Munch, Addi e M. Thompson, Alejandra Rougon-Cardoso, Daniel H. Chitwood, Robert VanBuren Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens...
Source: PLoS Biology: Archived Table of Contents - Category: Biology Authors: Source Type: research