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The "Biological Process" (BP GOO category comprises different types of metabolic processes, which in turn are the most represented subcategories.
The most represented subcategories assigned under "Biological Process" at third-level terms were: "primary metabolic process" (16.4%), "cellular metabolic process" (15.6%) and "macromolecule metabolic process" (14%).
Regarding MF GO categories (Additional file 2: Figure S2A and S3A), the catalytic and binding activities were the most represented subcategories for both up- and downregulated GO terms.
Metal ion, nucleic acid, and nucleotide binding are the most represented subcategories within the Binding activity category perhaps reflective of the need for biosynthetic and repair activity associated with rehydration of moss cells.
The most represented subcategories in the test set belonged to the catalytic activity, primary metabolic process and response to abiotic stimulus categories.To confirm that the observed variation within Col-3 replicates is independent from the variation in differential genes between Col-3, COX + and COX++, all significantly different genes were filtered out by ANOVA (α = 0.05).
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Binding (42.5%; 256/603) and catalytic activity (40.3%; 243/603) were the most highly represented subcategories within Molecular Function.
The most highly represented subcategories within Biological Process were cellular and metabolic processes, accounting for 32.4% (269/831) and 30.7% (255/831) of the transcripts respectively, in line with previous proteomic characterisation of the second generation merozoite [ 10].
The most highly represented subcategory was 'brain development' (GO 0007420), with 68 matches, and the second- and third-most frequent were 'spinal cord development' (GO 0021510) and 'central nervous system neuron differentiation' (GO 0021953), with 10 and 8 matches, respectively.
For the cellular component category, the most highly represented subcategory in roots and leaves was extracellular region part, while in stems, it was organelle and in flowers, it was extracellular region.
The five most represented pathway subcategories were: translation; energy metabolism; folding, sorting and degradation; carbohydrate metabolism; and amino acid metabolism.
The most represented GO subcategories within molecular function main term were binding (47%), catalytic activity (38.5%), transporter activity (4.8%), and transcription regulation activity (2.5%).
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