A) Schematic representation of pattern of change in gene expression when levels of total RNA in the two cells is similar. The square box represents a perturbation such as increased expression of a gene regulator or a change in environment or cell state. Red arrows point to target genes affected by the perturbation, which are represented as circles. Red shading of circles indicates relative transcriptional increase.
B) Schematic representation of microarray normalization when the overall levels of mRNA per cell are not changing in two conditions. Relative mRNA levels for 9 different genes (A–I) are indicated along the y-axis for condition 1 (black) and condition 2 (orange). The panels, from left to right, depict the actual relationship between mRNA levels for the two conditions; the effect of median normalization; the calculated fold-changes based on median normalization, with increased expression represented by red bars above the midline and decreased expression represented by green bars below the midline; and, the perceived transcriptional response of a limited transcriptional increase in gene expression.
C) Schematic representation of pattern of change in gene expression when levels of total RNA in the two cells is different such as in transcriptional amplification, where most genes are expressed at higher levels. The square box represents a perturbation such as increased expression of a gene regulator or a change in environment or cell state. Red arrows point to target genes affected by the perturbation, which are represented as circles. Red shading of circles indicates relative transcriptional increase.
D) Schematic representation of microarray normalization when the overall levels of mRNA per cell are increased in one condition compared to another. Relative mRNA levels for 9 different genes (A–I) are indicated along the y-axis for condition 1 (black) and condition 2 (orange). The panels, from left to right, depict the actual relationship between mRNA levels for the two conditions; the effect of median normalization; the calculated fold-changes based on median normalization, with increased expression represented by red bars above the midline and decreased expression represented by green bars below the midline; and, the perceived transcriptional response following transcriptional amplification of gene expression.