Its modular structure and possibilities to extend with additional functionalities through apps (formerly known as plugins) is discussed in “A travel guide to Cytoscape plugins”. A commonly used framework to visualise and analyse biological networks is Cytoscape. In addition, small molecules such as metabolites or drugs can play a role as regulators in cellular pathways.Ī systems biology approach in which interactions from different resources are combined, visualised and analysed together is an intuitive way to decipher complex biological processes. These modifications include phosphorylation, acetylation, palmitoylation and many more. Another group of regulatory effects are post-translational modifications which can influence protein activity.
They are able to influence the synthesis of many proteins or even those involved in entire pathways, making them important molecules in harmonised regulation. Upon binding miRNAs either repress translation or cleave the mRNA sequence. miRNAs are small, non-coding RNA molecules that bind to miRNA-target regions in the mRNA.
They either activate or repress transcription. TFs are proteins that bind to a specific DNA sequence, i.e., the transcription factor binding site (TFBS). Whereas gene expression is influenced by epigenetic factors and/or transcription factor (TF) binding, protein synthesis can be regulated by microRNAs (miRNAs). Regulation of gene expression, protein synthesis and activity occurs at different levels. These processes contain genes, proteins and/or metabolites, their molecular interactions and reactions, but little regulatory information is present. Many known biological processes are represented in various online repositories, like WikiPathways and Reactome. It still remains a challenge to combine the new insights with existing knowledge and to understand the regulation of biological processes in detail. Recently, the ENCODE project, whose main goal was to identify all the functional elements in the human genome sequence, revealed novel insights in genetic regulation. However, understanding of the regulation of gene expression, protein synthesis and activity is far from complete. Approximately 25,000 gene coding regions were defined. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist.Ĭompletion of the human genome project in 2003 generated a wealth of information about the human genetic code. No additional external funding was received for this study. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: This work was (co)financed by the Netherlands Consortium for Systems Biology (NCSB) which is part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research ( ).
Received: AugAccepted: OctoPublished: December 5, 2013Ĭopyright: © 2013 Kutmon et al. PLoS ONE 8(12):Įditor: Julio Vera, University of Erlangen-Nuremberg, Germany Citation: Kutmon M, Kelder T, Mandaviya P, Evelo CTA, Coort SL (2013) CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis.
0 kommentar(er)
