These results demonstrated that the microarray platform presented in this paper constitutes a complementary tool to the Affymetrix GeneChip for genome-wide transcriptomic analysis in citrus plants.
The highly reproducible results of the replicate data further validate the quality of the microarray platform and present dataset.
Using PamGene's 3-Dimensional, Flow-Through Microarray Platform we present a new format for MAPH: Microarray MAPH, using PMP22 gene dosage measurements in normal controls and CMT1A patients as an example.
The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species.
In total, this filtering approach yielded a gene set of 11,837 unique records, simultaneously present in all microarray platforms.
121 miRNAs present in both microarray platforms had no detectable measure by small RNA-seq in any of the three biological replicates, whereas 147 detected by small RNA-seq had not been addressed by any of the microarray platforms.
Furthermore, we found that 305 genes (286 in MRP1 and 272 in MRP2) were present across five microarray platforms, but were not detected by MPSS, neither from the 17-bp library nor the 20-bp library.
Expression values were used as features for the first classifier, either considering all genes present on both microarray platforms used, or the top 500 differentially expressed genes (available in Additional file 2).
Of the 78 ethylene-dependent (EIN2-dependent) leaf senescence-induced genes [ 28], 75 were present in both microarray platforms used, of which 25 (33%) were up-regulated in 2 DPA unfertilised pistils (Additional file 2).
These enrichment analyses were performed the same way as described before, except the background gene set used, which in this case is the set of all genes contained in the entire B cell network of Lefebvre et al. [ 36] which are also present on the microarray platforms investigated (n = 5,548).
For establishing the feature sets used in the random forest classification approach we considered only genes present on both microarray platforms of the two different studies (Affymetrix Human Genome U219 Array Plates in the case of the data of Kulis et al. and Affymetrix Human Genome U133A Arrays in the study of Fabris et al. n = 12,307).
