Although not studied systematically, interactions between some of the genes were present in the present study.
As shown in Figure 1C", 364 differentially-expressed genes were present between 4 M and PP.
Further statistical analysis revealed that 364 differentially-expressed genes were present between 4 M and PP (Fig. 1C").
The microarray results revealed that 1646 differentially-expressed genes were present between 4 M and 5 F (Fig. 1C) and 1276 between PP and 5 F (Fig. 1C').
Analysis of gene overlaps between the groups revealed that 5 genes were present in all groups, 14 genes overlapped between mPD and mN_fN, 53 genes overlapped between fPD and mN_fN, and 81 probesets (3.7% of all deregulated genes) were present in both mN_mPD and fN_fPD (Figure 1, Table S2).
However, it showed some variability between strains; for example, the T4SS genes were present in USDA 110T but were absent in CPAC 7 and USDA 6T.
Between the matched annotated genes in the two libraries, 7,349 (83%) genes were present in both libraries.
69 Other tools such as Bingo 70 and EnrichmentMap 71 can further construct a functional network, ie, a network in which nodes are genes and an edge between two genes is present if those genes share functional annotations.
This is coincident with findings that when distinct genes are present between samples with and without metastasis, they can also reflect differences between the HTB56 and A549 cell lines.
Whilst 1,629 annotated genes are common between the two strains, strain specific genes are present in both 0140J (145 genes present in 0140J not in EF20) and EF20 (222 genes present in EF20 not in 0140J) (Additional file 3 orthologous clustering).
