Download The study by E. Ivliev et al focusses on identifying new proteins

The study by E. Ivliev et al focusses on identifying new proteins involved in motile cilia
function. These cilia are reported to play a role in various human diseases. Analysing publicly
available gene array data leads to a list of proteins which are for the first time suggested to
play a role in motile cilia function. These are validated by looking at other publicly available
data including other gene array data, the protein atlas and the abstracts of articles by text
mining. Next to these new candidate proteins a possible relationship between some of these
cilia proteins and dyslexia was found. Although this could be explained by other functions of
these proteins (such as functions for the primary cilia). The study leads to sufficient new
knowledge while using publicly available data. The findings are in general represented in a
correct way and the methodology used can, as far as my knowledge goes, be considered as
appropriate for these kind of studies. The overlap and novelty of the findings is very elegantly
explained in the results and discussion section.
However, for improving the quality of this study and paper I would like to have more
information about the scoring of the protein expression with the help of the protein atlas.
Mainly how the objectivity of the scoring is guaranteed.
The presence of the MATE2 at the location of the motile cilia in itself can hardly be seen as a
proof of its functional relation with the motile cilia. More confirmative experiments are
necessary to reach this conclusion.
It can be considered as beyond the scope of the article, however, it could improve the validity
of the findings to have more confirmatory experiments of the findings. “Wet lab”
confirmation of the findings can greatly improve the impact of these findings and lead the
way for a more prominent role of this type of data analysis in protein discovery.
In the discussion I miss the relevance of finding the cilia candidate genes with weak
evidence. How much does finding them back in these study contribute to a possible
acceptance that the proteins these genes play a role in motile cilia?
The absence of certain golden standard motile cilia genes can be analysed further by really
identifying the reason for the absence at a gene to gene bases. This could help to identify
loopholes which prevent the discovery of other unknown cilia genes.The finding of dyslexia
is, as you mention, most likely related to its function in primary cilia (Increased expression of
the dyslexia candidate gene DCDC2 affects length and signaling of primary cilia in neurons.).
How this result influences the interpretation of the text mining or the specificity of the genes
for being involved in the primary cilia remains unclear.
Patrick von Morgen
0920150