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Table 4 A summary of the analogies between document-topic-word and a biological object in the relevant studies (see ““Document-word-topic” in biological data” section)

From: An overview of topic modeling and its current applications in bioinformatics

Reference Words Topics Documents Biological dataset
Rogers et al. (2005), Masada et al. (2009), Perina et al. (2010), Bicego et al. (2010a, b, 2012), Lee et al. (2014) Genes Functional groups Samples Expression microarray data
Masseroli et al. (2012), Pinoli et al. (2013, 2014), Youngs et al. (2014) Ontological terms Latent relationship Proteins Protein annotations
Chen et al. (2010, 2012a, b), La Rosa et al. (2015), Zhang et al. (2015) K-mers of DNA sequences Taxonomic category/components of the whole genome DNA sequences Genomic sequences
Caldas et al. (2009) Gene sets Biological process Experiments Gene expression dataset
Coelho et al. (2010) Object classes Fundamental patterns Images Fluorescence images
Konietzny et al. (2011) A fixed-sized vocabulary of words based on the gene annotations Functional modules of protein families Genome annotations A set of genome annotations
Bisgin et al. (2013) Endpoint measurements Diagnostic topics Drugs Expression of the HCS endpoints
Chen et al. (2011), Randhave and Sonkamble (2014) Functional elements (NCBI taxonomic level indicators, indicator of gene orthologous groups and KEGG pathway indicators) Functional groups Samples Genome set
Pan et al. (2010) Local sequential features Latent topic features Protein sequences Protein–protein interaction dataset
Castellani et al. (2010) Shape descriptors Brain surface geometric patterns Images Magnetic resonance images
Pratanwanich and Lio (2014) Genes Pathways Gene expression profiles Gene expression data
Dawson and Kendziorski (2012) Clinical events, treatment protocols, and genomic information from multiple sources The category of patients Patients Patient’s text constructed from clinical and multidimensional genomic analyses