Despite this, there is not a clear deletion pattern that is characteristic of a particular tumour type.
However, a clear deletion at OLFM4 correlated with a marked reduction in transcript levels in iCluster3 (log2FC 2.6) and, to a lesser extent, in iClusters1 and 4 (log2FC 1.9 and 1.7, respectively).
These proteins were proposed to be Sigma-54 dependent ([ 77] and [ 24], respectively), but considering the lack of compelling experimental evidence and the clear deletion within the 'GAFTGA' sequence (see additional file 3) they are probably not.
Despite this reduction in hybridisation ratio, however, it is clear that deletions and duplications (see below) show a change in ratio that is consistent with that seen for the X chromosome in the same experiment, which makes definition of the chromosome change relatively easy.
Apart from liver, poly(I C) mediated Cre-recombinase driven rac1 knockout was also observed in bone marrow, peripheral blood, lung, spleen, heart and kidney, whereas no clear rac1 deletion was detectable in the intestine and brain (Supplementary Table 3).
The exact role of EspK in virulence is not completely clear and deletion of its gene in M. bovis had no effect on virulence in a guinea pig infection model (Inwald et al., 2003).
When the structure of UvrD was determined it became clear that deletion of 102 C-terminal residues not only removes the entire C-terminal extension, it also deletes part of domain 2a, including a conserved motif that is involved in DNA binding [18].
However, it is not clear whether such deletions occur actively or result from passive homologous recombination.
It is not clear whether the deletions are associated with element loss.
There is a clear bias of deletions over insertions in CB4856, suggesting two possibilities.
