The functions of the identified genes cover various molecular functional categories which was the highest GO ontology, and the well-represented categories included ATP binding (GO 0005524) metal ion binding (GO 0046872), DNA binding (GO 0003677) zinc ion binding (GO 0008270), nucleotide binding (GO 0000166), protein binding (GO 0005515), and the structural constituent of ribosome (GO 0003735).
These sites cover a broad range of molecular functional categories, including 795 active sites, 1369 ligand binding sites, 1498 protein protein binding sites, 171 metal binding sites, 41 post-translational modification sites, and 113 sites with miscellaneous functions.
At level 2 of the gene ontology system, clusters were classified into 9 molecular functional categories, among which "binding" (GO 0005488) and "catalytic activity" (GO 0003824) categories were over-represented (95 and 82 clusters respectively).
Similarly, most of the molecular functional categories that emerged as significantly enriched are also groups of genes that participate in metabolic processes, e.g., exo- and metallopeptidases, hydrolases, and genes coding for o-methyltransferases, and carrier proteins (Table 3).
This analysis has revealed that the largest number of DNA replication and repair genes, 21.51% and 18.84% for rice and Arabidopsis respectively, fall into the DNA binding molecular functional categories.
We performed IPA (version 6.0; Ingenuity® Systems, Redwood City, CA, USA) [ 36] to find significant molecular functional categories enriched in the differentially expressed gene sets, and transformed the target genes into a set of relevant networks by using literature-based records that are maintained in the IPA Base.
Within the molecular functional category, 46% are related to protein binding followed by 32% catalytic activity.
Binding (31,859) and catalytic activities (25,935) were the most abundant groups within the molecular functional category.
In the molecular functional category, there was a higher number of down-regulated transcripts involved in nutrient reservoir and translation regulator activities in the heat-sensitive line compared with the heat-tolerant line.
GO term analysis of the genes with unique peaks in exons of the MTX-treated set with WebGestalt reveal that there is a weak enrichment of the molecular functional category methyltranferase activity, consistent with the role of MTX in the creation of SAM (Zhang et al. 2005).
Correlations between the molecular and functional categories are also provided in this compilation.
