COEXPNETVIZ

Comparative Co-Expression Network Construction and Visualization.
CoExpNetViz takes as input a set of bait genes chosen by you and at least one pre-processed gene expression dataset. You can also specify a negative and positive cutoff value, which will be used to determine if two genes are co-expressed or not.

CYCLUS3D

CyClus3D is a Cytoscape plugin for identifying functional modules in integrated networks composed of multiple interaction types. CyClus3D operates by clustering user-defined 3-node network motifs.

DIFFANY

We present an ontology-driven framework to infer and visualise an arbitrary set of condition-specific responses against a reference network. To this end, we have implemented algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardized methodology that allows a unified view on differential networks and promotes comparability between differential network studies.

EP3

EP3 is a tool for the identification of the core region of a eukaryotic gene promoter. It uses universal properties of the promoter to detect those regions in a whole genome context. EP3 has been tested on several eukaryotes ranging from protists to human. On human it is, at the moment, the best performing tool to identify regions that are associated with transcription initiation.