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United States Department of Agriculture

Agricultural Research Service

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: Net Venn - An integrated network analysis web platform for gene lists

Authors
item Wang, Yi -
item Thilmony, Roger
item Gu, Yong

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 8, 2014
Publication Date: April 25, 2014
Citation: Wang, Y., Thilmony, R.L., Gu, Y.Q. 2014. Net Venn - An integrated network analysis web platform for gene lists. Nucleic Acids Research. DOI: 10.1093/narlgku331.

Interpretive Summary: In many genomics projects, numerous big gene lists have been generated in order to address the biological significance of genes expression or protein interactions at different growth conditions and developmental stages. However, analysis of this big gene list data to identify the different and overlapping gene sets among gene lists has been an important task in bioinformatics. In this work, we developed NetVenn - an integrated interactome network-based web application for analysis of gene lists. This user-friendly web application tool not only allows for visualization of genes lists in the context of an interactome network with an interactive Venn diagram view, but it also directly links to a comprehensive annotation of the gene lists, thereby providing biological implications of these non-overlap and overlap gene sets among gene lists. To our knowledge, there are no other web-based tools containing all these features. NetVenn implementation on the World Wide Web makes it available for use on any computer with an internet connection independent of operating system and without the need to install programs locally. NetVenn can provide researchers with a powerful tool for analyzing and interpreting the biological meaning of genes from gene lists in the context of biological network.

Technical Abstract: Many lists containing biological identifiers such as gene lists have been generated in various genomics projects. Identifying the overlap among gene lists can enable us to understand the similarities and differences between the datasets. Here, we present an interactome network-based web application platform named NetVenn for comparing and mining the relationships among gene lists. NetVenn contains interactome network data publically available for several species and supports a user upload of customized interactome network data. It has an efficient and interactive graphic tool that provides a Venn diagram view for comparing two or more gene lists in the context of an interactome network. NetVenn also provides a comprehensive annotation of genes in the gene lists by using enriched terms from multiple functional databases. In addition, it allows for mapping the gene expression data, providing information of transcription status of genes in the network. The power graph analysis tool is included in NetVenn for simplified visualization of gene relationships in the network. NetVenn is freely available at http://probes.pw.usda.gov/NetVenn.

Last Modified: 10/23/2014
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