SICOP: identifying significant co-interaction patterns.

SUMMARY: Interactions between various types of molecules that regulate crucial cellular processes are extensively investigated by high-throughput experiments and require dedicated computational methods for the analysis of the resulting data. In many cases, these data can be represented as a bipartite graph because it describes interactions between elements of two different types such as the influence of different experimental conditions on cellular variables or the direct interaction between receptors and their activators/inhibitors. One of the major challenges in the analysis of such noisy datasets is the statistical evaluation of the relationship between any two elements of the same type. Here, we present SICOP (significant co-interaction patterns), an implementation of a method that provides such an evaluation based on the number of their common interaction partners, their so-called co-interaction. This general network analytic method, proved successful in diverse fields, provides a framework for assessing the significance of this relationship by comparison with the expected co-interaction in a suitable null model of the same bipartite graph. SICOP takes into consideration up to two distinct types of interactions such as up- or downregulation. The tool is written in Java and accepts several common input formats and supports different output formats, facilitating further analysis and visualization. Its key features include a user-friendly interface, easy installation and platform independence. AVAILABILITY: The software is open source and available at cna.cs.uni-kl.de/SICOP under the terms of the GNU General Public Licence (version 3 or later).

One plus one makes three (for social networks).

Members of social network platforms often choose to reveal private information, and thus sacrifice some of their privacy, in exchange for the manifold opportunities and amenities offered by such platforms. In this article, we show that the seemingly innocuous combination of knowledge of confirmed contacts between members on the one hand and their email contacts to non-members on the other hand provides enough information to deduce a substantial proportion of relationships between non-members. Using machine learning we achieve an area under the (receiver operating characteristic) curve (AUC) of at least 0.85 for predicting whether two non-members known by the same member are connected or not, even for conservative estimates of the overall proportion of members, and the proportion of members disclosing their contacts.

Understanding human navigation using network analysis.

We have considered a simple word game called the word-morph. After making our participants play a stipulated number of word-morph games, we have analyzed the experimental data. We have given a detailed analysis of the learning involved in solving this word game. We propose that people are inclined to learn landmarks when they are asked to navigate from a source to a destination. We note that these landmarks are nodes that have high closeness-centrality ranking.

Breaking the hierarchy--a new cluster selection mechanism for hierarchical clustering methods.

BACKGROUND: Hierarchical clustering methods like Ward's method have been used since decades to understand biological and chemical data sets. In order to get a partition of the data set, it is necessary to choose an optimal level of the hierarchy by a so-called level selection algorithm. In 2005, a new kind of hierarchical clustering method was introduced by Palla et al. that differs in two ways from Ward's method: it can be used on data on which no full similarity matrix is defined and it can produce overlapping clusters, i.e., allow for multiple membership of items in clusters. These features are optimal for biological and chemical data sets but until now no level selection algorithm has been published for this method. RESULTS: In this article we provide a general selection scheme, the level independent clustering selection method, called LInCS. With it, clusters can be selected from any level in quadratic time with respect to the number of clusters. Since hierarchically clustered data is not necessarily associated with a similarity measure, the selection is based on a graph theoretic notion of cohesive clusters. We present results of our method on two data sets, a set of drug like molecules and set of protein-protein interaction (PPI) data. In both cases the method provides a clustering with very good sensitivity and specificity values according to a given reference clustering. Moreover, we can show for the PPI data set that our graph theoretic cohesiveness measure indeed chooses biologically homogeneous clusters and disregards inhomogeneous ones in most cases. We finally discuss how the method can be generalized to other hierarchical clustering methods to allow for a level independent cluster selection. CONCLUSION: Using our new cluster selection method together with the method by Palla et al. provides a new interesting clustering mechanism that allows to compute overlapping clusters, which is especially valuable for biological and chemical data sets.