title: Retrieving relevant time-course experiments: a study on Arabidopsis microarrays.
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.
authors.affiliation: Department of Computer Engineering, Başkent University, Baglica Campus TR-06810, Ankara, Turkey. ddede@baskent.edu.tr.
authors.forename: Duygu Dede
authors.initials: DD
authors.lastname: Şener
authors.affiliation: Department of Computer Engineering, Başkent University, Baglica Campus TR-06810, Ankara, Turkey.
authors.forename: Hasan
authors.initials: H
authors.lastname: Oğul
mesh_terms: D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D013997:Time Factors
chemical_list: D029681:Arabidopsis Proteins