Netview is a free web tool that allow end users to explore the human and mouse gene regulatory networks. Users can query the system by providing a gene identifier and the boundaries of the subnetwork being explored. The system provides the list of interactions, the enriched Gene Ontology Terms together with a graphical representation of the subnetwork.
GenCLiP is a literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. GenCLiP can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords.
polyadq is a program for detection of human polyadenylation signals. To avoid training on possibly flawed data, the development of polyadq began with a de novo characterization of human mRNA 3′ processing signals. This information was used in training two quadratic discriminant functions that polyadq uses to evaluate potential polyA signals.
FirstEF (First Exon Finder) is a 5′ terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. The probabilistic models are optimized to find potential first donor sites and CpG-related and non-CpG-related promoter regions based on discriminant analysis. For every potential first donor site (GT) and an upstream promoter region, FirstEF decides whether or not the intermediate region can be a potential first exon, based on a set of quadratic discriminant functions.
PhenoPred is a web-based tool designed to detect novel gene-disease associations in humans. It is based on known gene-disease associations, protein-protein interaction data, protein functional annotation at a molecular level and protein sequence data. Machine learning principles are used to integrate heterogeneous data sources. PhenoPred can be used to prioritize genes based on their likelihood to be associated with a given disease or to prioritize diseases for a given query gene.