CellFateScout – a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction

Cell Communication and Signaling

Methodology

Georg Fuellen¹  Marcin Siatkowski²  Volkmar Liebscher³ 

[1] Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Ernst Heydemann Strasse 8, D-18057, Rostock, Germany;Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Ernst Heydemann Strasse 8, D-18057, Rostock, Germany;DZNE, German Center for Neurodegenerative Disorders, Gehlsheimer Strasse 20Germany, D-18147, Rostock;Institute for Mathematics and Computer Science, University of Greifswald, Jahnstr. 15a, D-17487, Greifswald, Germany;

关键词: Small molecules;    Drug repositioning;    Cell transformation;    Induction of pluripotency;    Cell fate;    Bioinformatics tool;    Pathway database;   

DOI  :  10.1186/1478-811X-11-85

 received in 2013-07-29, accepted in 2013-10-29,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundSmall molecule effects can be represented by active signaling pathways within functional networks. Identifying these can help to design new strategies to utilize known small molecules, e.g. to trigger specific cellular transformations or to reposition known drugs.ResultsWe developed CellFateScout that uses the method of Latent Variables to turn differential high-throughput expression data and a functional network into a list of active signaling pathways. Applying it to Connectivity Map data, i.e., differential expression data describing small molecule effects, we then generated a Human Small Molecule Mechanisms Database. Finally, using a list of active signaling pathways as query, a similarity search can identify small molecules from the database that may trigger these pathways. We validated our approach systematically, using expression data of small molecule perturbations, yielding better predictions than popular bioinformatics tools.ConclusionsCellFateScout can be used to select small molecules for their desired effects. The CellFateScout Cytoscape plugin, a tutorial and the Human Small Molecule Mechanisms Database are available at https://sourceforge.net/projects/cellfatescout/ under LGPLv2 license.

【 授权许可】

Unknown   
© Siatkowski et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.