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Reconstruction and Comparison of Cellular Signaling Pathway Resources for the Systems-Level Analysis of Cross-Talks

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Systems Biology

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Abstract

Signaling pathways control a large variety of cellular processes and their defects are often linked with diseases. Reliable analyses of these pathways need uniform pathway definitions and curation rules applied to all pathways. Here, we compare KEGG, Reactome, Netpath and SignaLink pathway databases and examine their usefulness in systems-level analysis. Further on, we show that the integration of various bioinformatics databases allows a comprehensive understanding of the regulatory processes that control signaling pathways. We also discuss the drug target relevance of cross-talking (i.e., multi-pathway) proteins and signal transduction regulators (e.g., phophatases and miRNAs). Accordingly, modern integrated databases are not only essential for studying signaling processes at the systems level, but will also serve as invaluable tools for pharmacology and network-based medicine.

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Abbreviations

HTP:

High-throughput

PPI:

Protein-protein interaction

TF:

Transcription factor

TFBS:

Transcription factor binding site

miRNA:

microRNA

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Acknowledgments

The authors thank the members of the NetBiol Group (http://netbiol.elte.hu) for their useful comments and Peter Csermely for discussions. Work of TK was supported by a János Bolyai Scholarship of the Hungarian Academy of Sciences.

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Authors and Affiliations

  1. Department of Genetics, Eötvös Loránd University, Budapest, Hungary

    Máté Pálfy, László Földvári-Nagy, Dezső Módos & Tamás Korcsmáros

  2. Department of Morphology and Physiology, Faculty of Health Sciences, Semmelweis University, Budapest, Hungary

    Dezső Módos & Katalin Lenti

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  1. Máté Pálfy
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  2. László Földvári-Nagy
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Correspondence to Tamás Korcsmáros .

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Editors and Affiliations

  1. Chemical and Biological Engineering, Vanderbilt University, Nashville, TN, USA

    Aleš Prokop

  2. Research Group on Process Network Engineering, Kaposvár University, Kaposvár, Hungary

    Béla Csukás

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Pálfy, M., Földvári-Nagy, L., Módos, D., Lenti, K., Korcsmáros, T. (2013). Reconstruction and Comparison of Cellular Signaling Pathway Resources for the Systems-Level Analysis of Cross-Talks. In: Prokop, A., Csukás, B. (eds) Systems Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6803-1_16

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