@ Ulster University, Northern Ireland
Tailored bioinformatics tools for neuromuscular function & disease.
Most bioinformatics tools and data resources are designed to have wide application, whereas more tailored approaches can provide analyses that are adapted to specific pathologies or tissue types. We have developed several systems biology tools for neuromuscular research, accessible through the Sys-Myo website (http://sys-myo.rhcloud.com/).
These tools include: (i) CellWhere – when given a list of genes/proteins, CellWhere returns a network map of gene functional associations overlaid onto a schema of the cell and its subcellular compartments. CellWhere can be used to help formulate mechanistic hypotheses and to screen data for proteins that may be at specific cell compartments. (ii) Muscle Gene Sets – public transcriptomic data are used to create lists of genes that were differentially expressed across muscle experiments and pathologies, to be used for gene enrichment testing. (iii) The Dystrophin Interactome – this tool combines public functional association data with new proteomic experimental data on the binding partners of Dystrophin, enabling exploration of the interactions of this important muscle protein with other cellular components. (iv) MyoMiner – this database summarizes gene co-expression across previous microarray studies of muscle tissues and pathologies, potentially yielding a new empirically-derived definition of functional gene clusters in muscle.