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and varying experimental conditions (e.g. transfected/transduced cells, cytokine stimulated, cells under hypoxic conditions, ultraviolet treated cells, cells treated with chemotherapeutics or non cytotoxic drugs etc).. Probesets that were available on both platforms were converted to official gene symbols, averaging expression values of multiple probesets targeting the same gene.
In the case of multiple probesets targeting an individual protein, the probeset with the highest expression was selected to represent that protein.
Furthermore, our method of averaging the signal value of multiple probesets targeting the same transcript on the U133 Plus 2 is only a rough compromise.
The redundancy offered by Exon arrays, which feature multiple probesets targeting individual exons along the length of each gene provide a robust platform for dealing with the uncertainties of RNA extracted from FFPE material.
For each alternative splicing event, MADS+ evaluates the P-values of multiple probesets targeting exons and exon exon junctions, requiring opposite trends for probesets targeting competing isoforms as evidence of differential splicing.
As these data represent the median values for multiple probesets targeting the length of the gene, it is probable that the RNA degrades along the entire length of the TP63 transcript.
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This disparity in numbers results because the U133 Plus 2 array frequently has multiple independent probesets targeting the same transcript cluster, whereas the probesets are clustered and summarized into a single gene signal estimate on the exon array.
These results demonstrate that probesets targeting multiple genes can be separated in two groups, a major group targeting genes with strong sequences similarities or close proximity, and a group of probesets targeting genes without clear biological evidence.
This can result in probesets targeting transcripts of multiple genes due to low probe specificity, probes that do not map any of the known transcripts [ 41, 42] or multiple probesets that map the same gene [ 39, 40], requiring the development of methods used for the validation of existing probes and for probeset redefinition [ 41, 42, 96].
Therefore we created additional probesets targeting microRNAs and included these in our analysis.
For this microarray, Affymetrix identified eight probesets targeting the Surf4 gene.
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