A series of online tools to query gene expression datasets and inferred functional gene networks have been developed in collaboration with computer scientists and web developers.
Seed eFP Browser
This page can be used to pictographically visualize gene expression in seeds across a range of publicly available datasets, and was published as part of Bassel et al. 2008, Plant Physiology. You can access this web tool here. This was developed together with Dr. Nick Provart at The University of Toronto.
Using the publicly available data in the eFP browser, the gene co-expression network SeedNet was generated. This network predicts genome-wide gene interactions in each dormant and germinating Arabidopsis seeds (Bassel et al. 2011, PNAS).
The online queryable interface for SeedNet enables users to identify the position of gene(s) of interest within the network while establishing their co-expressed partners specifically in seeds. This approach was used to identify 11 novel regulators of seed germination in the original publication and will serve as a valuable template for additional hypothesis generation. SeedNet online can be accessed here.
SCoPNet is a genome-wide network model generated using the rule-based machine learning algorithm BioHEL (Bassel et al. 2011, The Plant Cell). Functional associations between genes are established by the collective ability to come together and form “rules” that accurately predict developmental outcome in seeds.
An online web-queryable version of SCoPNet can be found here.