PathBLAST: a tool for alignment of protein interaction networks

Abstract

PathBLAST is a network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. The basic method searches for high-scoring alignments between pairs of protein interaction paths, for which proteins of the first path are paired with putative orthologs occurring in the same order in the second path. This technique discriminates between true- and false-positive interactions and allows for functional annotation of protein interaction pathways based on similarity to the network of another, well-characterized species. PathBLAST is now available at http://www.pathblast.org/ as a web-based query. In this implementation, the user specifies a short protein interaction path for query against a target protein-protein interaction network selected from a network database. PathBLAST returns a ranked list of matching paths from the target network along with a graphical view of these paths and the overlap among them. Target protein-protein interaction networks are currently available for Helicobacter pylori, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. Just as BLAST enables rapid comparison of protein sequences between genomes, tools such as PathBLAST are enabling comparative genomics at the network level.

Figure 1

Identifying conserved protein interaction pathways with PathBLAST. PathBLAST operates in two modes, depending on whether the query is a single pathway or a whole network. In the first mode, single user-defined pathways are queried against a reference network of observed protein interactions from bacteria, yeast, fly or worm. In the second mode, two large protein networks are aligned against each other to enumerate all of the pathways that are conserved between them. High-scoring pathway matches (A–D) are ranked by score and indicate pathways that are potentially conserved over evolution. The current focus of the PathBLAST website is on the first (more common) mode of query.

Figure 2

PathBLAST front page. To define the pathway query, users enter a series of protein IDs (DIP number, common name, or systematic ORF designation), or a series of FASTA-format protein sequences, each with a corresponding sequence identifier. The length of the query pathway can be varied between two and five proteins by using the ‘Add a Protein’ and ‘Remove a Protein’ buttons. Users must specify the BLAST E-value threshold for protein sequence similarity (used to determine which protein pairs should be considered as putative orthologs) as well as the target network for comparison. As part of a brief tutorial, users can evaluate the approach on several example pathways.

Figure 3

Example of PathBLAST search result. The pathway (Ste20-Act1-Myo1) was used to query the yeast protein–protein interaction database for high-scoring pathway alignment matches. Each matching protein is linked to a functional annotation, if available.

Figure 4

Linked graphical representation. Each pathway alignment is hyperlinked to a graphical representation which, if applicable, shows other high-scoring aligned paths that overlap the present alignment. These overlapping paths are connected in the target network and may shed light on higher order pathway bifurcations or protein complexes of interest. The query pathway (Ste20-Myo1-Act1) is shown on the left in green. Matches from the target network are shown on the right, with relative score encoded by color so that the best scoring match is red, the second best is purple and so on according to the score key at bottom. For instance, the best scoring match in the upper display is (Cmk2-Myo5-Arp3). Solid edges indicate direct protein–protein interactions in the network database, whereas dashed lines indicate gapped alignments (see text).