NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules

Summary: The prioritization of candidate disease genes is often based on integrated datasets and their network representation with genes as nodes connected by edges for biological relationships. However, the majority of prioritization methods does not allow for a straightforward integration of the user’s own input data. Therefore, we developed the Cytoscape plugin NetworkPrioritizer that particularly supports the integrative network-based prioritization of candidate disease genes or other molecules. Our versatile software tool computes a number of important centrality measures to rank nodes based on their relevance for network connectivity and provides different methods to aggregate and compare rankings. Availability: NetworkPrioritizer and the online documentation are freely available at http://www.networkprioritizer.de. Contact: mario.albrecht@mpi-inf.mpg.de

[1]  Stephen P. Borgatti,et al.  Centrality and network flow , 2005, Soc. Networks.

[2]  Bart De Moor,et al.  A guide to web tools to prioritize candidate genes , 2011, Briefings Bioinform..

[3]  Tariq Ahmad,et al.  Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci , 2010, Nature Genetics.

[4]  Duc-Hau Le,et al.  GPEC: A Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection , 2012, Comput. Biol. Chem..

[5]  Lili Wang,et al.  iCTNet: A Cytoscape plugin to produce and analyze integrative complex traits networks , 2011, BMC Bioinformatics.

[6]  D. Saari.  Explaining All Three-Alternative Voting Outcomes , 1999 .

[7]  Fidel Ramírez,et al.  Novel search method for the discovery of functional relationships , 2011, Bioinform..

[8]  Fidel Ramírez,et al.  Computing topological parameters of biological networks , 2008, Bioinform..

[9]  Falk Schreiber,et al.  Exploration of biological network centralities with CentiBiN , 2006, BMC Bioinformatics.

[10]  Moni Naor,et al.  Rank aggregation methods for the Web , 2001, WWW '01.

[11]  Thomas Lengauer,et al.  Improving disease gene prioritization using the semantic similarity of Gene Ontology terms , 2010, Bioinform..

[12]  Mario Albrecht,et al.  Recent approaches to the prioritization of candidate disease genes , 2012, Wiley interdisciplinary reviews. Systems biology and medicine.

[13]  John Skvoretz,et al.  Node centrality in weighted networks: Generalizing degree and shortest paths , 2010, Soc. Networks.

[14]  Hong Zhu,et al.  Oxidative stress and redox signaling mechanisms of inflammatory bowel disease: updated experimental and clinical evidence , 2012, Experimental biology and medicine.

[15]  Ravinder Singh,et al.  Fast-Find: A novel computational approach to analyzing combinatorial motifs , 2006, BMC Bioinformatics.

[16]  Chung-Yen Lin,et al.  Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology , 2008, Nucleic Acids Res..

[17]  Wenfei Fan,et al.  Keys for XML , 2001, WWW '01.

[18]  Nadezhda T. Doncheva,et al.  Topological analysis and interactive visualization of biological networks and protein structures , 2012, Nature Protocols.