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The sequences that had recognizable homologs constituted 937 InterProScan and 494 Gene Ontology terms (Additional files 5 and 6), indicating that a great diversity of protein motifs and biological processes was represented in our dataset.
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A total of 16 subgroups of biological processes are represented (Figure 7, lower middle chart).
In the Gene Ontology (GO) tree, enriched Gene Ontology biological processes are represented by connected nodes with an associated statistical significance (P values derived from a hypergeometric hypothesis test in BiNGO).
Seven different biological processes were represented, being "cell growth and maintenance" the most frequent class (Fig. 1a).
Few biological processes were represented by more than one gene, and clear patterns of gene ontology were not apparent.
To determine which biological processes are represented among those genes that are not represented in the Arabidopsis multinetwork, a MIPS functional category analysis was carried out (Table 2c).
Many biological processes were represented including metabolism, response to stress or stimulus, development, transport and signal transduction, although unknown was the most common (42%).
To evaluate which biological processes are represented within the obtained probe set list, the differentially expressed genes were annotated with the Gene Ontology (GO) terms.
Functional classification of the identified proteins is summarized in table 1, where almost all categories and major biological processes are represented.
In addition, many other genes belonging to calcium-related biological processes were represented in the CCA data (Additional file 5: CCA).
We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com