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The recent influx in generation, storage and availability of textual data presents researchers with the challenge of developing suitable methods for their analysis. Latent Semantic Analysis (LSA), a member of a family of methodological approaches that offers an opportunity to address this gap by describing the semantic content in textual data as a set of vectors, was pioneered by researchers in psychology, information retrieval, and bibliometrics. LSA involves a matrix operation called singular value decomposition, an extension of principal component analysis.LSA generates latent semantic dimensions that are either interpreted, if the researcher's primary interest lies with the understanding of the thematic structure in the textual data, or used for purposes of clustering, categorisation and predictive modelling, if the interest lies with the conversion of raw text into numerical data, as a precursor to subsequent analysis. This paper reviews five methodological issues that need to be addressed by the researcher who will embark on LSA. We examine the dilemmas, present the choices, and discuss the considerations under which good methodological decisions are made. We illustrate these issues with the help of four small studies, involving the analysis of abstracts for papers published in the European Journal of Information Systems.

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Gene regulatory networks (GRNs) control development via cell type-specific gene expression and interactions between transcription factors (TFs) and regulatory promoter regions. Plant organ boundaries separate lateral organs from the apical meristem and harbor axillary meristems (AMs). AMs, as stem cell niches, make the shoot a ramifying system. Although AMs have important functions in plant development, our knowledge of organ boundary and AM formation remains rudimentary. Here, we generated a cellular-resolution genomewide gene expression map for low-abundance Arabidopsis thaliana organ boundary cells and constructed a genomewide protein–DNA interaction map focusing on genes affecting boundary and AM formation. The resulting GRN uncovers transcriptional signatures, predicts cellular functions, and identifies promoter hub regions that are bound by many TFs. Importantly, further experimental studies determined the regulatory effects of many TFs on their targets, identifying regulators and regulatory relationships in AM initiation. This systems biology approach thus enhances our understanding of a key developmental process.