Among the upregulated genes in our dataset, transcripts encoding ERBB4 were ∼10-fold increased in CHLA-10 compared to CHLA-9 cells (Fig 1; p = 0.015).
For this dataset, transcripts were included in the analysis if the intensity was above the median signal intensity of negative control spots present on the array, and in addition, the minimum intensity was 250 units in at least one sample-point.
In all four datasets, transcripts associated with tandem duplicated genes showed dramatically increased variance across perturbations and genotypes in comparison to the whole genome (Figure 1).
For both 1KG and ESP datasets, transcripts in the GENCODE Comprehensive geneset overlap with more variants in all broad groups of consequences than RefSeq NXR transcripts.
As with previous datasets shuffling the transcript dataset abrogated this signal (not shown).
This revealed that real-time qPCR was about two magnitudes more sensitive than that provided by their SAGE dataset, allowing transcript quantities as low as 0.00075 copies per cell to be measured.
Spring embedding was used to investigate further the relationships between time points in the dataset of transcript profiles [ 37].
However, filtering of the present dataset for transcript variants encoding proteins involved in ROS-related processes should identify candidate ESTs for further characterization.
In the 454 dataset, one transcript (contig 00133) annotated as strictosidine β-D-glucosidase in C. roseus (CrSGD) was identified with a predicted homologous peptide of 178 amino acids.
Blastn searches with the unmatched A. glycines dataset (45,706 transcripts) revealed hits for 4,576 transcripts, with top hits to A. pisum (2,931/4,576) and Aphis craccivora (1,381/4,576).
