Skip to main content

Table 2 Association of differentially expressed genes in co-expression clusters (see Figure 2) with GO functional categories

From: Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice

  Percentage of transcripts classified in co-expression profiles in Figure 2.
Functional Categories High to low Low to high PMA, MA, SCP, TPA PMA, MA, SCP MA SCP TPA  
  1 2 3 4 5 6 7 8 9 10 Total
Amino acid metabolism 0.6 1.6 1.1 1.4 1.8 0.8 1.1 0.3 0.2 0.6 1.2
Carbohydrate metabolism 0.8 2.0 1.2 4.4 1.4 3.4 2.5 1.1 1.4 1.6 2.0
Catalytic activity 1.7 2.7 2.4 4.8 3.8 6.8 5.7 4.0 3.0 3.9 3.5
Cell cycle 2.3 3.3 6.1 2.1 2.3 1.2 1.2 1.6 0.7 1.3 3.0
Cell structure 1.7 2.0 3.0 1.7 1.4 2.4 2.6 2.2 2.5 5.4 2.5
Chromatin remodeling 1.7 2.7 2.5 1.3 1.0 1.0 0.7 0.5 0.4 0.6 1.7
Energy metabolism 1.5 3.6 1.6 4.7 1.8 3.4 3.0 2.7 2.5 1.3 2.7
Lipid metabolism 1.1 2.2 2.5 3.6 3.0 6.6 4.4 3.0 4.6 2.6 2.9
Nucleotide metabolism 0.6 1.3 1.6 1.5 1.1 0.0 0.7 0.0 0.7 0.4 1.1
Protein-protein interaction 2.3 3.3 2.7 4.4 2.3 2.8 2.6 2.7 4.0 2.1 3.0
Protein metabolism 5.7 7.9 6.3 6.8 7.3 4.4 6.3 8.9 11.6 4.0 6.9
RNA metabolism 7.7 7.5 7.4 2.2 3.8 1.2 1.9 1.1 1.4 1.0 4.8
Secondary metabolism 1.8 0.6 0.9 0.9 1.2 3.8 4.0 3.2 5.3 2.7 1.7
Signal transduction 6.6 7.5 8.8 9.0 8.2 7.8 9.3 7.8 6.8 10.5 8.3
Stress 4.4 3.1 3.0 3.5 3.7 6.6 6.5 4.0 5.1 4.6 3.8
Transcription factors 8.9 8.0 7.7 5.3 5.1 7.0 7.6 8.9 6.1 5.7 7.1
Translation 1.1 8.8 2.8 1.5 1.3 0.2 1.0 0.0 0.7 0.2 3.4
Transporters 2.3 4.1 3.5 4.8 5.5 7.8 4.4 4.0 5.4 6.2 4.5
Vesicular trafficking 0.3 2.9 1.0 5.0 2.4 2.6 0.7 0.0 0.4 2.2 2.1
Others 46.9 25.1 33.9 31.1 41.3 30.5 34.0 44.1 37.5 43.1 33.8
Genes in each cluster 652 3124 2439 1383 1068 502 733 372 571 1071 11915
  1. The total representation of genes (% values) of three major functional categories (besides 'Others') is shown in bold & underlined text. Over-representation of genes in each functional category by more than 20% of their overall representation in individual clusters is highlighted with bold and italicized letters.