All styryl compounds in the particular library analyzed in this study shared the same molecular scaffold and therefore possessed many features in common (Figure 2).
In such a comparison 114 genes were regulated in common (Figure 2).
For the eight growth factors evaluated the cellular processes affected in common (Figure 5) included changes in cell contact, morphogenesis, and cell proliferation and differentiation.
Based on bioinformatics analysis 75 genes were regulated exclusively in dysplasia (Supplementary Figure S5 and Supplementary Text S1), where as 387 genes could be attributed to adenocarcinoma of which 39 genes were regulated in common (Figure 15).
18 haplotypes were observed in total (8 for susceptible and 12 for resistant, with 2 haplotypes in common) (Figure 3) and have been submitted to Genbank (Accession number HM193720-HM193437).
Excluding the 30 genes identified as having general roles in antibiotic susceptibility (see below), only antibiotics of the same class have a substantial number of beneficial or deleterious transposon insertion locations in common (Figure 3).
Second, C. taiwanensis (Ctai) and C. eutrophus H16 (Ceut) have more genes in common (Figure 3) i.e., are more closely related than is the case for the other Cupriavidus species, confirming the findings of Amadou et al. [46].
Two replicates for the AcH3 ChIP-chip experiment were sufficient because they were highly reproducible – of 1,388 regions identified within the two replicates, 1,189 (>90%) were in common (Figure 1A).
Many of the gene sets from different oncogenic signature pathways shared significant overlap (Figure 1I), yet, interestingly, each pathway set associated uniquely with its corresponding oncogene; for example, the EGFR and erbB-2 signatures had many genes in common (Figure 1B), yet the EGFR signature genes did not associate with mRNA patterns of erbB-2 in the human data, and vice versa (Figure 2B).
We identified 84 SAGE tags to be down-regulated in CIS relative to both BE and PC (Table S9), and 48 SAGE tags to be down-regulated in invasive SCC relative to both BE and PC (Table S10), with 31 tags in common (Figure 3B).
