Abstract
Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Although existing data exploration tools are available for single study data exploration, no tool provides all the required functionality for multistudy data exploration. We have therefore used the Kvik framework to develop Kvik Pathways, an application for exploring gene expression data in the context of biological pathways. We have used Kvik Pathways to explore data from both a cross-sectional study design and a case-control study within the Norwegian Women and Cancer (NOWAC) cohort. Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.In this note, we describe how we used the Kvik framework to develop the Kvik Pathways application. Kvik Pathways was used by our team of epidemiologists toexplore gene expression data from healthy women with high and low plasma ratios of essential fatty acids.
Highlights
Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies
An existing tool may be useful for one project, no tool provides the required functionality for several different projects
Through pathway visualizations and integration with the Kyoto encyclopedia of genes and genomes (KEGG) databases, epidemiologists can perform targeted exploration of pathways and genes to get an overview of the biological functions that are involved with gene expression from the underlying dataset
Summary
Any reports and responses or comments on the article can be found at the end of the article. The initial version Kvik[1] contained a prototype system for exploring biological pathways and gene expression data From this prototype we built the Kvik Framework, which provides developers a simple interface to powerful systems for statistical analyses and meta-databases, and Kvik Pathways: a publicly available data exploration application. To understand the results it is important to have instant access to existing knowledge from online databases Familiar They should use familiar visual representations to present information to researchers. In Kvik Pathways researchers can explore gene expression data from 7 combined with information from online knowledge bases. Kvik Pathways, a publicly available web application for exploring gene expression data in the context of biological pathways without any additional applications than a web browser. A detailed description of how we have used Kvik Pathways to explore gene expression data from healthy women with high and low plasma ratios of essential fatty acids
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