BIOL368/F14:Chloe Jones Week 12

Getting to know your microarray data

For the microarray experiment they collected and used samples form MRSA-252.
They hybridized 6 microarray chips in this experiment
The paired samples on the chip were: Control 1 and Ranaflexin 1, Control 2 and Ranaflexin 2, Control 3 and Ranaflexin 3
Cy5 and Cy3 were both used for each individual technical replicate.
In this experiment they performed three biological replicates, with each having two technical replicates for a total of six.
The paper used ImaGene to quantify the florescence signal in each spot, calculate the ratio of red/green, and to transform the ratio to log (base2).
The paper used GeneSpring v7 to normalize the log ratios as well as perform statistical analysis.
To compare against known data, used mapping GO annotations, only reference to known data that was proven by them (discovery-driven experiment)
The UniProt GO mapping for Staphylococcus aureus was used to assign GO terms to the reference datasets. Fisher exact test was performed for every GO term associated with each of the test datasets(TU, TD, PU, PD)
Because this was discovery-driven experiment they only were able to map the microarray data based on its own pathway