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

  • Máté Pálfy
  • László Földvári-Nagy
  • Dezső Módos
  • Katalin Lenti
  • Tamás Korcsmáros


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.


Signaling Cross-talk Regulation Drug discovery Network Pathway miRNA Drug targeting Pathway database 





Protein-protein interaction


Transcription factor


Transcription factor binding site





The authors thank the members of the NetBiol Group ( 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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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Máté Pálfy
    • 1
  • László Földvári-Nagy
    • 1
  • Dezső Módos
    • 1
    • 2
  • Katalin Lenti
    • 2
  • Tamás Korcsmáros
    • 1
  1. 1.Department of GeneticsEötvös Loránd UniversityBudapestHungary
  2. 2.Department of Morphology and PhysiologyFaculty of Health Sciences, Semmelweis UniversityBudapestHungary

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