Detection of gene orthology from gene co-expression and protein interaction networks

Background Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes across different pathways, and understanding the evolution of gene families. Results We exploit features derived from the alignment of protein-protein interaction networks and gene-coexpression networks to reconstruct KEGG orthologs for Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository and Mus musculus and Homo sapiens and Sus scrofa gene coexpression networks extracted from NCBI\u27s Gene Expression Omnibus using the decision tree, Naive-Bayes and Support Vector Machine classification algorithms. Conclusions The performance of our classifiers in reconstructing KEGG orthologs is compared against a basic reciprocal BLAST hit approach. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit

A Process-Centric Data Mining and Visual Analytic Tool for Exploring Complex Social Networks

Social scientists and observational scientists have a need to analyze complex network data sets. Examples of such exploratory tasks include: finding communities that exist in the data, comparing results from different graph mining algorithms, identifying regions of similarity or dissimilarity in the data sets, and highlighting nodes with important centrality properties. While many methods, algorithms, and visualizations exist, the capability to apply and combine them for ad-hoc visual exploration or as part of an analytic workflow process is still an open problem that needs to be addressed to help scientists, especially those without extensive programming knowledge. In this paper, we present Invenio-Workflow, a tool that supports exploratory analysis of network data by integrating workflow, querying, data mining, statistics, and visualization to enable scientific inquiry. Invenio-Workflow can be used to create custom exploration tasks, in addition to the standard task templates. After describing the features of the system, we illustrate its utility through several use cases based on networks from different domains. 1