Comparison of AlignNemo and NetAligner.

<p>The two algorithms are evaluated in terms of recovering known protein complexes in both (CYC2008) and (CORUM). Solutions matching known complexes are scored by means of precison, recall, and F₁ score.</p

The edges incident to a node are ranked according to the their score.

<p>A value plotted on the curve is the average over all nodes of the alignment graph of the scores of the edges of the same rank incident to the nodes. To have comparable distribution of values, we select all the nodes on the union graph with at least 100 edges. The black curve corresponds to the human-fly alignment graph with 1578 nodes and the red curve to the yeast-fly alignment graph with 9325 nodes. Independent of the aligned networks, scores decrease exponentially making the pruning step both essential and effective.</p

AlignNemo Overview.

<p>Given two input PPI networks (1) the alignment graph is built and scores are assigned to its nodes and edges (2). Then <i>seeds</i>, i.e. small subgraphs with a large number of high scoring links and nodes, are extracted from the alignment graph (3), and each seed is expanded in a greedy fashion, by adding small subgraphs that are relatively well connected to it by reliable links (4).</p

Statistics on the size of the union graph and alignment graph.

<p>For the alignment graph two cases are considered: when there is a correction of the weights assigned to edges due to multiple orthologs (as in our experiments) and when this correction is not applied.</p

Example of union graph.

<p>The union graph includes both <i>composite</i> nodes representing pairs of homologous proteins from the two species (light blue nodes), and <i>simple</i> nodes representing the proteins that do not have an homolog in the other network (red and green nodes). Similarly, both composite interactions (black edges) and interactions present in only one species (red and green edges) are present in the union graph.</p

Comparison of AlignNemo, NetworkBLAST, and Mawish.

<p>The three algorithms are evaluated in terms of recovering known protein complexes in both (CYC2008) and (CORUM). Solutions matching known complexes are scored by means of precison, recall, and F₁ score. Obtained score distributions for each method are plotted in panel (A) for yeast-fly alignment, and panel (B) for human-fly alignment. Panels (C) and (D) show the average semantic similarity between proteins from different species mapped by each solution. Each solution is represented by a circle with the radius proportional to the size of the solution. The size of the solutions from each method varies significantly, thus small (<7 nodes) and big ( 7 nodes) solutions are shown separately. * Percentages refer to the set of complexes matched by at least one method.</p

Comparison of AlignNemo, Mawish, NetworkBLAST, and NetAligner.

<p><b>No. of S.</b>: Number of Solutions; <b>M.S.</b>: Matching Solutions; <b>S.C.R.</b>: Small Complex Recovered.</p><p>The number of solutions found by each algorithm (No. of S.) is listed in column 2 and 5 for the yeast-fly and the fly-human alignment, respectively. The number of solutions that match at least one known complex is reported in columns 3 and 6 (M.S. - Matching Solutions) for each alignment. The number of high-quality matches for complexes of size 4 is summarized in columns 4 and 7 (), while the number of small complexes (2-3 proteins) recovered is in columns 5 and 8 (S.C.R. - Small Complex Recovered).</p

A synopsis on network alignment tools.

*<p>All methods, as a last step, score and rank the solutions according to a similarity function.</p

Workflow for the performance evaluation of network inference methods on a proteomic dataset.

<p>The workflow is comprised of a computational inference component and a pathway knowledgebase component that are used to generate separate PPI network models. Caveats involved in Steps 1–6 are discussed in Discussion and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004765#pcbi.1004765.s001" target="_blank">S1A Text</a>.</p

PANCAN11 tumor types, the abbreviations used in the study, and the number of samples in each tumor type.

<p>PANCAN11 tumor types, the abbreviations used in the study, and the number of samples in each tumor type.</p