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Fig. 1 | BMC Bioinformatics

Fig. 1

From: GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Fig. 1

Overview of the GOexpress workflow. A typical GOexpress analysis takes as input: an ExpressionSet of the Biobase Bioconductor package containing either microarray or RNA-seq normalised expression data; the name of an experimental factor present in the phenoData slot of the ExpressionSet; and annotations for the features and GO terms (or other functional classes) considered. The GO_analyse function calculates scores and ranks for the individual genes and GO terms. Optionally, the pValue_GO function randomly permutes the gene features to estimate the probability of each GO term to rank (or score) higher by chance. Finally, various functions allow visualisation of gene expression profiles by gene and gene ontology, and export of the calculated statistics in text files

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BMC Bioinformatics

ISSN: 1471-2105

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