Retrieving relevant time‐course experiments: a study on Arabidopsis microarrays. Issue 3 (1st June 2016)

• Record Type: Journal Article
• Authors: Şener, Duygu Dede; Oğul, Hasan
• Is Part Of: IET systems biology. Volume 10:Issue 3(2016)
• Page Start: 87
• Page End: 93
• Publication Date: 2016-06-01
• Subjects: botany -- lab‐on‐a‐chip -- genetics -- bioinformatics -- information retrieval -- data mining -- data analysis -- associative processing; relevant time‐course experiment retrieval -- time‐course Arabidopsis microarray -- time‐course gene regulation -- stimulus response -- systems biology -- computational method -- gene behaviour model -- gene networked interaction -- latent parameter -- model parameter estimation -- meta‐analysis -- data analysis -- time‐course gene expression experiment -- information retrieval -- computational framework -- time‐course experiment query -- relevant experiment list -- repository -- environmental factor -- query experiment -- experimental content similarity; Systems biology -- Periodicals; Cell physiology -- Periodicals; Biological systems -- Mathematical models -- Periodicals; Genetics -- Mathematical models -- Periodicals; Computational biology -- Periodicals; 573
• DOI: 10.1049/iet-syb.2015.0042
• Languages: English
• ISSNs: 1751-8849

Abstract

Abstract : Understanding time‐course regulation of genes in response to a stimulus is a major concern in current systems biology. The problem is usually approached by computational methods to model the gene behaviour or its networked interactions with the others by a set of latent parameters. The model parameters can be estimated through a meta‐analysis of available data obtained from other relevant experiments. The key question here is how to find the relevant experiments which are potentially useful in analysing current data. In this study, the authors address this problem in the context of time‐course gene expression experiments from an information retrieval perspective. To this end, they introduce a computational framework that takes a time‐course experiment as a query and reports a list of relevant experiments retrieved from a given repository. These retrieved experiments can then be used to associate the environmental factors of query experiment with the findings previously reported. The model is tested using a set of time‐course Arabidopsis microarrays. The experimental results show that relevant experiments can be successfully retrieved based on content similarity.