Related Experiment Video
Updated: May 9, 2026
11:19
Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
Published on: November 17, 2019
Reconn: a cytoscape plug-in for exploring and visualizing reactome
Willem P A Ligtenberg1, Dragan Bošnački, Peter A J Hilbers
1BioModeling and BioInformatics, Department of BioMedical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands. W.P.A.Ligtenberg@tue.nl
Journal of Bioinformatics and Computational Biology
|July 18, 2013
Summary
ReConn is a new tool that overcomes limitations of static biological pathway visualizations. It enables flexible analysis of large biological datasets across multiple levels, offering dynamic pathway generation and exploration.
Area of Science:
- Systems Biology
- Bioinformatics
- Computational Biology
Background:
- Existing biological pathway visualization tools offer static representations, limiting analysis flexibility.
- These tools lack consensus on pathway elements, dynamic pathway generation, and integration of multiple biological system levels.
Purpose of the Study:
- To present ReConn (Reactome Connector), an open-source interface and visualization tool for flexible analysis of large biological data at multiple levels.
- To address the limitations of static pathway representations by enabling dynamic pathway generation, selective views, and multi-level data integration.
Main Methods:
- ReConn is an extension for Cytoscape, facilitating user-friendly interaction with the Reactome database.
- It supports using predefined Reactome pathways, generating new pathways from metabolites, extending existing pathways, and retrieving alternative routes.
- The tool integrates information from multiple biological system levels into a single view.
Main Results:
- ReConn allows users to generate novel pathways and extend existing ones by adding related reactions.
- It enables the retrieval of alternative routes within biological networks, useful for knockout experiment design.
- The tool provides dynamic visualization of biological pathways, integrating multiple system levels.
Conclusions:
- ReConn overcomes the limitations of static biological pathway visualization tools.
- It offers a flexible and dynamic approach for analyzing large biological datasets across multiple levels.
- The tool enhances biological network analysis and experimental design, such as knockout studies.
Related Concept Videos
01:17Coupled Reactions
Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions.
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions. Cells...
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions. Cells...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...