Paolo Ciccarese, Stefano
Mazzocchi.
Thanks to
Lucia
Sacchi and Fulvia
Ferrazzi
2004
IDAMAP 2004
Genius: a new tool for gene networks visualization.
Paolo Ciccarese,
Stefano Mazzocchi, Fulvia Ferrazzi, Lucia Sacchi.
Intelligent Data Analysis in Medicine & Pharmacology Proceedings, ed Blaz
Zupan, John H. Holmes , pag. 107 - 111.
Genius is a graphical software tool for visualizing genetic networks composed by a high number of genes. It accepts as input a matrix summarizing gene relationships inferred by means of reverse engineering methods. Genius offers two visualization modalities (the Agorà style and the TouchGraph style), that can be exploited in a complementary way. It is thus possible to obtain a clear and easily customizable view of one or more networks of interest which allows to simplify the exploration of the inferred relationships.
It is a graphical software tool for visualizing genetic networks composed by a high number of genes. It accepts as input a matrix summarizing gene relationships inferred by means of reverse engineering methods.
Data are organized by row, thus, the gene "G005" influences the genes: "G001" and "G002".
These oriented relations are depicted through two different kind of graphs:
1) The next graph comes from an idea of Stefano Mazzocchi. It was originally used for visualization of virtual community through a run-time interactive molecular-style simulation. For more details on the implemented model, visit the web site of the project (Agorà).
After a simulation, we will obtain the following layout:
2) The second kind of graph is based on TouchGraph and is more oriented to show influences of a particular gene (the yellow one). In the following picture are depicted first level influences:
Depicting second level influences too:
The entire network inferred from the serum response data as displayed after the automatic process which rearranges nodes according to their force of attraction/repulsion. Nodes whose label is highlighted are the so called "hubs", that is the most highly connected pseudo-genes (indicated with the numbers 13, 85, 161, 169).
Genius was born as prototype and was presented in IDAMAP 2004 (paper). At the moment I am not planning future development as Stefano and I developed Welkin a graph-based RDF visualizer (read more about Agorà, Genius and Welkin history in the Stefano's blog).
