List2Net: Linking multiple lists of biological data in a network context.

Motivation: A common task in scientific research is the comparison of lists or sets of diverse biological entities such as biomolecules, ontologies, sequences and expression profiles. Such comparisons rely, one way or another, on calculating a measure of similarity either by means of vector correlation metrics, set operations such as union and intersection, or specific measures to capture, for example, sequence homology. Subsequently, depending on the data type, the results are often visualized using heatmaps, Venn, Euler, or Alluvial diagrams.

PathIN: an integrated tool for the visualization of pathway interaction networks.

PathIN is a web-service that provides an easy and flexible way for rapidly creating pathway-based networks at several functional biological levels: genes, compounds and reactions. The tool is supported by a database repository of reference pathway networks across a large set of species, developed through the freely available information included in the KEGG, Reactome and Wiki Pathways database repositories. PathIN provides networks by means of five diverse methodologies: (a) direct connections between pathways of interest, (b) direct connections as well as the first neighbours of the given pathways, (c) direct connections, the first neighbours and the connections in between them, and (d) two additional methodologies for creating complementary pathway-to-pathway networks that involve additional (missing) pathways that interfere in-between pathways of interest.

PathExNET: A tool for extracting pathway expression networks from gene expression statistics.

A fundamental issue related to the understanding of the molecular mechanisms, is the way in which common pathways act across different biological experiments related to complex diseases. Using network-based approaches, this work aims to provide a numeric characterization of pathways across different biological experiments, in the prospect to create unique footprints that may characterise a specific disease under study at a pathway network level. In this line we propose PathExNET, a web service that allows the creation of pathway-to-pathway expression networks that hold the over- and under expression information obtained from differential gene expression analyses.