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LENS: Web-based lens for enrichment and network studies of human proteins

Handen, A and Ganapathiraju, MK (2015) LENS: Web-based lens for enrichment and network studies of human proteins. BMC Medical Genomics, 8 (4).

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Abstract

© 2015 Handen and Ganapathiraju. Background: Network analysis is a common approach for the study of genetic view of diseases and biological pathways. Typically, when a set of genes are identified to be of interest in relation to a disease, say through a genome wide association study (GWAS) or a different gene expression study, these genes are typically analyzed in the context of their protein-protein interaction (PPI) networks. Further analysis is carried out to compute the enrichment of known pathways and disease-associations in the network. Having tools for such analysis at the fingertips of biologists without the requirement for computer programming or curation of data would accelerate the characterization of genes of interest. Currently available tools do not integrate network and enrichment analysis and their visualizations, and most of them present results in formats not most conducive to human cognition. Results: We developed the tool Lens for Enrichment and Network Studies of human proteins (LENS) that performs network and pathway and diseases enrichment analyses on genes of interest to users. The tool creates a visualization of the network, provides easy to read statistics on network connectivity, and displays Venn diagrams with statistical significance values of the network's association with drugs, diseases, pathways, and GWASs. We used the tool to analyze gene sets related to craniofacial development, autism, and schizophrenia. Conclusion: LENS is a web-based tool that does not require and download or plugins to use. The tool is free and does not require login for use, and is available at http://severus.dbmi.pitt.edu/LENS.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Handen, A
Ganapathiraju, MKmadhavi@pitt.eduMADHAVI
Date: 9 December 2015
Date Type: Publication
Journal or Publication Title: BMC Medical Genomics
Volume: 8
Number: 4
DOI or Unique Handle: 10.1186/1755-8794-8-s4-s2
Schools and Programs: School of Medicine > Biomedical Informatics
Refereed: Yes
Date Deposited: 18 Aug 2016 19:47
Last Modified: 30 Mar 2019 12:55
URI: http://d-scholarship.pitt.edu/id/eprint/28940

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