To minimize the possibility of missing a potential pathogenic abnormality, all CNVs (≥25 kb) involving one or more of the genes described in the Online Mendelian Inheritance in Man (OMIM) Morbid Map were reported, even when, according to the clinical information, they were detected in apparently healthy individuals.
See Additional file 1 for a more exhaustive list of genes described in this study.
Given the fact that PTBP1 has been shown to regulate alternative splicing of numerous other genes not previously implicated in cholesterol metabolism [13], [14], [15], our findings raise the possibility that sterols influence alternative splicing on a more global scale beyond the genes described here.
This response is only present at 40 50°C; it involves among others the fla/che operon, the lytA-C genes for autolysis and genes encoding methyl accepting chemotaxis proteins mcpA- B. Surprisingly, the heat-induced transcriptional response also includes a number of sporulation and competence genes, described in more detail below.
Merkej et al [ 12] found that free living bacteria with larger genomes often have more genes that are described as virulence factors than pathogenic bacteria, challenging many early hypotheses that the presence of particular virulence factors was predictive of the pathogenicity of an organism [ 12].
Only 18 GO categories are attributed to 1000 or more genes; from these, five describe some molecular 'binding', and seven refer to cellular components.
Based on the same criteria described before, many more genes were found to be differentially expressed.
When the Pl TT01 genome was first sequenced, it was described as having more genes encoding toxins than any other genome sequenced to date [ 16].
The redundancy evident in the toxin gene repertoire of Photorhabdus and Xenorhabdus is astounding – at the time of its sequencing in 2003, P. luminescens was described as having more genes encoding toxins than any other genome sequenced to date [ 40], however, Serratia sp. SCBI also has over 200 genes encoding toxins, NRPS genes, multiple drug efflux systems and assorted virulence factors.
The annotation of each gene is therefore a potentially long laborious process, which for a highly studied gene like TNF could take several days (Fig. 2) or, for a more recently described gene like CDKN2B, may only take a few hours (Fig. 1).
