Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

Abstract

The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files.

Trends in the Application of “Omics” to Ecotoxicology and Stress Ecology

“…For example, exposure to hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) elicited a conserved mode of action throughout phylogenetically remote organisms [65]. Identifying conserved expression patterns (or pathways of toxicity (PoT) [12]) requires concerted functional analyses based on gene set enrichment, network modeling, text mining, graph-based, and pathway enrichment analyses [68][69][70][71][72][73][74][75]. For example, in the field of phenomics, ontology-based semantic mapping (OS-Mapping) has been used to identify chemical by species interactions and similar mechanisms of action (MOAs) across species [76,77].…”

A novel algorithm for alignment of multiple PPI networks based on simulated annealing

“…Global network alignment provides an effective computational framework to systematically identify functionally *Correspondence: jhu@nwpu.edu.cnorshang@nwpu.edu.cn 1 School of Computer Science, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China Full list of author information is available at the end of the article conserved proteins from a global node map between two or more protein-protein interaction (PPI) networks [18][19][20]. These alignments of two networks are called pairwise network alignment [21,22]. These of more than two are termed as multiple network alignment [23][24][25].…”