Among them, the three most representative pathways were metabolic pathways (2,857 members), spliceosome (805 members) and biosynthesis of plant hormones (644 members) (Additional file 4).
The most representative pathways by the unigenes were 'metabolic pathways' (3,500 members), 'starch and sucrose metabolism' (1,344 members) and 'biosynthesis of secondary metabolites' (1,196 members).
We directly find the most representative pathways in each scenario and enumerate top-ranked paths according to an objective function based on actual gene expression/protein data.
The most representative pathways were metabolic pathways (5704 unigenes; 13.72%), followed by the cancer (5704; 3.8%), focal adhesion (1469; 3.5%), regulation of actin cytoskeleton (1289; 3.1%), and RNA transport pathways (1221; 2.9%).
A detailed examination of the most representative pathways related to these 730 predicted target genes showed a significant overrepresentation for "HIF-1 signaling pathway (hsa04066)", "Acute myeloid leukemia (hsa05221)", "Colorectal cancer (hsa05210)", "Renal cell carcinoma (hsa05211)" and "Type II diabetes mellitus (hsa04930)" (Additional file 5: Figure S1).
In clear consistency with the generated networks, the most representative canonical pathway significantly modulated between groups was the LXR/RXR activation (p-value = 6.19 × 10-10) (Table 4), which regulates the whole de novo FA synthesis pathway.
All the most representative KEGG pathways mapped to ES proteins shown in table 3 are required for parasite survival inside the host, as the secretome of a parasite is representative of its genome in the host environment.
Using feature selection within each such cluster, we use the most representative features within each pathway.
The CCmedian group revealed overexpression of genes involved in insulin signaling pathway, the most representative being IGFBP3, IGFBP5 and PIK3R1.
Most representative unigenes were mapped to specific pathways, such as metabolism pathways, biosynthesis of secondary metabolites, plant-pathogen interactions, the spliceosome, and starch and sucrose metabolism, using the KEGG database (Additional file 2).
