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Out of the 113 published genes, none met our filtering criteria of 1.5-fold change in two or more consecutive time-points.
In sciatic nerve endoneurium, 331 probes met our filtering criteria as being differentially regulated in at least two consecutive time-points (Table 1).
None of the cholesterol metabolism related genes tested in our experiment met our filtering criterion of 1.5-fold change in two consecutive conditions (for example see Cyp51, Dhcr7, Lss, Nsdhl, Sc4 mol, Sqle; Fig. S4).
On average, 96.066% of nucleotide sites on the third chromosome met our filtering criteria for each individual D. pseudoobscura strain (see Supporting Information, Table S1).
Ultimately, 12,177 genes with expression values measured for 19 samples (10 mice with DR and 9 controls) met our filtering criteria and were included in the meta-analysis step.
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The remaining 99,471 contigs lack a high confidence SNP that meets our filtering criteria.
Although the remaining 24 putative SNPs showed polymorphism between lines, they had low coverage (<10 reads) and did not meet our filtering criteria (at least 20 reads), therefore were not included in our final SNP dataset from the IGA transcriptome assembly.
For explorative data analysis, however, it is more convenient to plot an overall overview as a first step before devisively splitting up the variance (Fig. 5a). Figure 2 shows all traits meeting our filter-constraints, both projected by CA (Fig. 2a) and hierarchically clustered (Fig. 2c).
Of the 1337 proteins that were identified, 202 proteins met our stringent filtering criteria – the expression of 112 proteins was increased in Rab18 −/− mice (supplementary material Table S2), and the expression of 90 proteins was decreased (supplementary material Table S3) in Rab18 −/− sciatic nerves.
Of the 54,210 transcripts represented on the chip, 25,986 met our present/absent filter criterion.
None of these six genes met our less stringent filtering criterion of 1.5-fold change in two or more consecutive time-points, indicating that neither expression of sodium channels nor that of neurotrophin associated genes were affected by the onset of type 1 diabetes.
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