To account for differences in starting material, RNA preparation, RNA quality and cDNA synthesis, adequate normalisation is frequently performed by comparing expression profiles of the genes of interest with those of constitutively expressed genes (= reference genes).
Here, by comparing expression profiles between SE and NE lineages, we observed that uncommitted progenitor cells, expressing stem cell markers, are present in the neural plate border/neural fold prior to neural tube closure.
Since deletion of Otx2 leads to a total loss of photoreceptors in the retina, by comparing expression profiles between the Otx2 CKO retina and control retina, we were able to identify photoreceptor-associated genes more clearly than by using other mutant retinas.
By comparing expression profiles with Drosophila melanogaster we also assessed which genes are well conserved within the Diptera versus those that are more recently evolved.
The variability of expression profiles in bronchial biopsies was assessed by comparing expression profiles obtained from control subjects to each other (figure 1A, r2 = 0.94 and data not shown).
We used whole genome expression arrays to identify Pax8-regulated genes by comparing expression profiles of Pax8-silenced PCCl3 cells with both scrambled siRNA-treated and wild type (wt) PCCl3 cells.
We applied Significance Analysis of Microarrays (SAM, version 1.21) [ 21] to analyze the differential expression of genes by comparing expression profiles of pog1Δ, ptp1-1, or ptp2-1 withethe wild type.
Finally, by comparing expression profiles between cell types, we have identified sets of transcripts that are lineage specific and show, in an accompanying manuscript, the expression and function of 4 novel proteins in arterial thrombus formation.
By comparing expression profiles of laser-capture microdissected mammary tumors, we identify Glis1 as a transcription factor that is highly expressed in the subset of tumors with elevated Wnt gene expression.
Some investigators have tried to identify a set of genes related to radiosensitivity by comparing expression profiles of radiosensitive and radioresistant tumours obtained as clinical samples before treatment using a cDNA microarray (Hanna et al, 2001; Kitahara et al, 2002).
