However, microRNA microarray data generated from the same amount of total RNA were not normalized in general, because we know that the amount of microRNA varies depending upon cell types, such as normal tissue vs. cancer [15].
Microarray data generated using A. thaliana subjected to NaCl stress were obtained from a previous report (Dinneny et al. 2008).
B, The CACGTGTC motif (containing the ABRE consensus) attained the highest MAMA score when microarray data generated from Arabidopsis roots subjected to NaCl stress were analyzed.
C, The CGACCGAC motif (which contains a DRE) attained the highest MAMA score when human microarray data generated from Arabidopsis roots subjected to NaCl stress were analyzed.
A, The TGGCGACA motif (containing a ZDRE) attained the highest MAMA score when microarray data generated from rice roots subjected to zinc deficiency were analyzed.
Therefore, SplicerEX provides an important tool for the biologist interested in studying changes in mRNA isoform usage from conventional or splice-sensitive microarray platforms, especially considering the expansive amount of archival microarray data generated over the past decade.
All microarray data generated is compliant with current MIAME standards according to Brazma et al [22].
The quality of microarray data generated in this study is excellent for identifying differentially expressed genes.
The miRNA and mRNA microarray data generated by this study are available in the NCBI Gene Expression Omnibus (GEO) as series accession identifier GSE21514.
Microarray data generated in this study meet Minimum Information about Microarray Experiment (MIAME) standards and are available at ArrayExpress [43] under accession number E-TABM-700.
Although the presence of repetitive elements within the first exons was informative about alternative promoter evolution, our subsequent analyses dealt with microarray data generated from DAlFE transcripts.
