Stability Indicators in Network Reconstruction

• DOI: 10.1371/journal.pone.0089815
• Publication Date: 2014-02-27T23:54:47Z
• Authors: Michele Filosi; Roberto Visintainer; Samantha Riccadonna; Giuseppe Jurman; Cesare Furlanello
• Keywords: 0301 basic medicine; Carcinoma, Hepatocellular; Science; Molecular Networks (q-bio.MN); 0206 medical engineering; 610; 02 engineering and technology; Models, Biological; 03 medical and health sciences; Yeasts; Humans; Quantitative Biology - Molecular Networks; Gene Regulatory Networks; Settore BIO/11 - BIOLOGIA MOLECOLARE; Q; Liver Neoplasms; R; 004; MicroRNAs; FOS: Biological sciences; Medicine; Neural Networks, Computer; Algorithms; Research Article

The number of algorithms available to reconstruct a biological network from a dataset of high-throughput measurements is nowadays overwhelming, but evaluating their performance when the gold standard is unknown is a difficult task. Here we propose to use a few reconstruction stability tools as a quantitative solution to this problem. We introduce four indicators to quantitatively assess the stability of a reconstructed network in terms of variability with respect to data subsampling. In particular, we give a measure of the mutual distances among the set of networks generated by a collection of data subsets (and from the network generated on the whole dataset) and we rank nodes and edges according to their decreasing variability within the same set of networks. As a key ingredient, we employ a global/local network distance combined with a bootstrap procedure. We demonstrate the use of the indicators in a controlled situation on a toy dataset, and we show their application on a miRNA microarray dataset with paired tumoral and non-tumoral tissues extracted from a cohort of 241 hepatocellular carcinoma patients.