This finding is of major importance for the interpretation and design of future microarray experiments with adult Daphnia.
We illustrate the inference technique to obtain the value of the parameter p from microarray experiments with a specific example.
Our microarray experiments with neonatal hypothalami, however, revealed no consistent changes of any of these genes after food deprivation at P5. We, therefore, tested the expression of these candidate genes by real-time RT-PCR, and found no significant changes in expression levels in P5 hypothalami after fasting in either WT or Snord116del samples (Fig. 2C).
We introduced two additional parameters to improve co-expression inferences: a threshold for the minimum observed change in mRNA levels across the set of array experiments (R in Table 2), and a threshold for the minimum number of microarray experiments with expression values greater than R (M in Table 2).
Microarray experiments with at least 2 replicates were taken.
We kept the genes which have microarray experiments with at least 3 replicates.
This method, however, does not discriminate between individual microarray experiments with or without associated biases.
DAB conceived, analysed and designed the study, performed microarray experiments with BF, and wrote the paper.
AW performed infection of cell lines, FACS and microarray experiments with statistical analysis.
Due to the scarcity of time course microarray experiments with uniform design, gene expression datasets with different designs were used.
We designed a microarray using human single copy genes and conducted microarray experiments with mRNAs extracted from the squid.
