Abstract
Adipogenesis is the process of cell differentiation by which mesenchymal stem cells become adipocytes. Extensive research is ongoing to identify genes, their protein products, and microRNAs that correlate with fat cell development. The existing databases have focused on certain types of regulatory factors and interactions. However, there is no relationship between the results of the experimental studies on adipogenesis and these databases because of the lack of an information center. This information fragmentation hampers the identification of key regulatory genes and pathways. Thus, it is necessary to provide an information center that is quickly and easily accessible to researchers in this field. We selected and integrated data from eight external databases based on the results of text-mining, and constructed a publicly available database and web interface (URL: http://210.27.80.93/arn/), which contained 30873 records related to adipogenic differentiation. Then, we designed an online analysis tool to analyze the experimental data or form a scientific hypothesis about adipogenesis through Swanson’s literature-based discovery process. Furthermore, we calculated the “Impact Factor” (“IF”) value that reflects the importance of each node by counting the numbers of relation records, expression records, and prediction records for each node. This platform can support ongoing adipogenesis research and contribute to the discovery of key regulatory genes and pathways.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0321-0) contains supplementary material, which is available to authorized users.
Highlights
Adipose tissue is an important site for lipid storage, energy homeostasis, and whole-body insulin sensitivity
Growth of adipose tissue is the result of differentiation of new fat cells from precursor cells [1]
Testing hypotheses Once we have many hypotheses, which may be obtained by the Adipogenic Regulation Network (ARN)-Analysis tool, we may want to determine which is the most important by initially screening out nodes that are highly correlated with adipogenesis
Summary
Adipose tissue is an important site for lipid storage, energy homeostasis, and whole-body insulin sensitivity. Testing hypotheses Once we have many hypotheses, which may be obtained by the ARN-Analysis tool, we may want to determine which is the most important by initially screening out nodes that are highly correlated with adipogenesis For this purpose, we calculated the “IF” value for each node with the following formula: IFðiÞ 1⁄4 1⁄2Ri=Rmax þ Ei=Emax þ Pi=Pmax=3 Â 100%. Basic information of the ARN database Currently, the database contains 3054 nodes (genes and microRNAs), 1807 relation records, 1141 summary records, 10675 expression records, and 43 review images associated with adipogenesis according to 1457 papers. Researchers can first obtain the throughput article’s PMID in the “ARN-literature page” (see Additional file 2: Handbook of ARN, Example 2), and use "Filter By Expression" to analyze it. The same method can be used to analyze the other top 50 nodes
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