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. 2012:8:47-60.
doi: 10.4137/EBO.S8018. Epub 2011 Dec 18.

SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis

Dimosthenis Tsagrasoulis  1 , Vasilis Danos, Maria Kissa, Philip Trimpalis, V Lila Koumandou, Amalia D Karagouni, Athanasios Tsakalidis, Sophia Kossida
Affiliations

SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis

Dimosthenis Tsagrasoulis et al. Evol Bioinform Online. 2012.

Abstract

Domain Fusion Analysis takes advantage of the fact that certain proteins in a given proteome A, are found to have statistically significant similarity with two separate proteins in another proteome B. In other words, the result of a fusion event between two separate proteins in proteome B is a specific full-length protein in proteome A. In such a case, it can be safely concluded that the protein pair has a common biological function or even interacts physically. In this paper, we present the Fusion Events Database (FED), a database for the maintenance and retrieval of fusion data both in prokaryotic and eukaryotic organisms and the Software for the Analysis of Fusion Events (SAFE), a computational platform implemented for the automated detection, filtering and visualization of fusion events (both available at: http://www.bioacademy.gr/bioinformatics/projects/ProteinFusion/index.htm). Finally, we analyze the proteomes of three microorganisms using these tools in order to demonstrate their functionality.

Keywords: BLAST; gene fusion; protein protein interactions.

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Figures

Figure 1
Figure 1
Screenshot of the FED database homepage, showing the available search options.
Figure 2
Figure 2
Workflow of the SAFE software. Starting with the input FASTA files of the proteomes of the two organisms that the user wants to analyse, userspecified parameters are used in different steps to filter the data, as described in the text. The output files of the program can be downloaded as text files or visualised on the SAFE interface, as shown in Figure 3.
Figure 3
Figure 3
The SAFE interface. On the bottom right is the graphical representation of the selected results.
Figure 4
Figure 4
Examples of fusion events detected by SAFE. (A) A protein from the species Entamoeba histolytica with suggested cytidyltransferase activity, generated by a Fusion Event. (B) A tRNA synthetase protein from the species Thermofilum pendens, generated by a Fusion Event. (C) A protein from the species Entamoeba histolytica that has methionyl-tRNA synthetase activity, generated by a Fusion Event. (D) A composite mannose transferase which is found fused in Aquifex aeolicus proteome.
See this image and copyright information in PMC

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