WebGIVI: a web-based gene enrichment analysis and visualization tool
Date
2017-05-04
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BioMed Central
Abstract
BACKGROUND: A major challenge of high throughput transcriptome studies is presenting the data to researchers in
an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for
enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate
genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining
system. However, examining large lists of iTerm and gene pairs is a daunting task.
RESULTS: We have developed WebGIVI, an interactive web-based visualization tool (http://raven.anr.udel.edu/webgivi/)
to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can
be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used
to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs
using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports
uploading and visualization of any two-column tab separated data.
CONCLUSIONS: WebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering,
sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition,
WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research
publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI. The WebGIVI
tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php.
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Citation
Sun et al. BMC Bioinformatics (2017) 18:237 DOI 10.1186/s12859-017-1664-2