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Lists2Networks: integrated analysis of gene/protein lists
Alexander Lachmann1, Avi Ma'ayan
1Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA.
BMC Bioinformatics
|February 16, 2010
Summary
Systems biologists can now easily analyze large-scale omics data using Lists2Networks. This web-based system integrates gene and protein lists with biological knowledge for hypothesis generation.
Area of Science:
- Systems biology
- Bioinformatics
- Computational biology
Background:
- Analyzing large-scale omics data from diverse experiments presents a significant challenge for systems biologists.
- Integrating data from various sources like gene expression, proteomics, and phosphoproteomics requires a coherent framework.
- Linking experimental results with prior biological knowledge aids in identifying functional themes and generating hypotheses.
Purpose of the Study:
- To develop a user-friendly, web-based system for integrated analysis of multi-omics data.
- To facilitate the comparison and manipulation of gene/protein lists from different biological studies.
- To enable the expansion of gene lists using biological networks and knowledge bases.
Main Methods:
- Developed Lists2Networks, a web-based system for uploading and analyzing mammalian gene/protein lists.
- Implemented tools for list manipulation (set operations) and expansion using protein-protein interaction, co-expression, and co-annotation networks.
- Integrated gene-list enrichment analyses against various biological knowledge libraries (pathways, Gene Ontology, miRNA targets, etc.).
Main Results:
- Lists2Networks allows integrated analysis of multiple gene/protein lists against numerous biological knowledge bases.
- Users can expand gene lists using protein-protein interaction, co-expression, and co-annotation correlations.
- The system supports exporting networks and sharing analysis lists among users.
Conclusions:
- Lists2Networks is a user-friendly, web-based software designed to simplify computational analysis for systems biologists.
- The system supports high-throughput experiments across multiple layers of biological regulation.
- Lists2Networks is freely accessible at http://www.lists2networks.org.
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