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One important aspect was to determine which genes could be used to differentiate between tumour and normal tissues based on expression analysis (Table 2).
This work led us to postulate a role for several genes in sporopollenin synthesis and deposition, and transcriptional regulation of pollen development processes, based on expression analysis and previous works in model species.
Some of these studies have proposed a different developmental origin for these two subgroups based on expression analysis of established tumours (Fukuzawa et al., 2009; Gadd et al., 2012).
It may not be informative, however, to make a prognosis based on expression analysis performed on the heterogeneous cell populations within early-stage primary tumors, in which metastatic cells may not be present or may represent only a rare subset of the total tumor mass.
The reference miRNA (miR-26b, MS00009233; miR-92-1, MS00006594 and SNORD61-1, MS00033705, QIAGEN Pty Ltd ,Doncaster, Australia)) were selected based on expression analysis using the geNorm component of the qBase relative quantification analysis software [ 56], because their expression was stable across samples [ 57].
The reference genes (ribosomal protein P0 [ 59], phosphoglycerate kinase 1 [ 60] and peptidylprolyl isomerase A [ 60]) were chosen based on expression analysis using the geNorm component of the qBase relative quantification analysis software [ 56, 61], because their expression was stable across samples [ 57].
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To identify groups of genes associated with meristem development, we performed a clustering analysis based on expression profiles and the GO analysis of the resulting data.
The two C-clade genes GAGA1 and GAGA2 have been considered similar in their function based on expression patterns and transgenic analysis.
Some of the genes that were highly amplified were also differentially expressed based on the expression analysis of frequently gained regions, so we also included genes with a log fold change greater than 0.6 (n = 17).
This procedure is based on gene expression analysis and exploits the inverse correlation existing between the expression behavior of a host gene and the target genes of the corresponding intragenic miRNA.
Based on RNA expression analysis, TR4 target genes are generally expressed.
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