Abstract       Introduction        Materials and Methods       Results      Discussion      Sources Cited

Oxidative stress is involved in many human diseases but is a natural product of metabolism. ZMS1 and ZMS2 are repressors for the ZWS gene which is involved in combating oxidative stress. In this experiment microarrays were used to study what genes were influenced by the knockout of the ZMS genes to find more genes involved in oxidative stress.

Slide 096

    No useable data was obtained from the hybridization of green labeled wild type cDNA and red labeled zms2 DNA. This could have been due a variety of reasons. The RNA could have been degraded by RNases before reverse transcription, or due to the lack of results on all slides, the reverse transcriptase could have failed. Another possibility might be an improperly prepared buffer that could have resulted in a failed hybridization. Whatever the cause, no data was obtained from slide 096.

Slide 725, 726, 695

    The analysis of slides 725, 726, and 695 resulted in a list of three unregulated genes. Two of the three up-regualted genes have unknown roles (YBR284W and YFL049W). YFL049W is involved in gene regulation by altering DNA packaging. Either of these genes could be involved in oxidative stress, although further research is needed to confirm this.  The third up-regulated gene is a tubulin folding factor that does not seem like it should be involved in oxidative stress, though subsequent testing may lead to new findings.

    There were ninety-six down regulated genes, but only the most down-regulated genes were included in this study. There were three genes which were down regulated below -1.5.  Two of these genes are involved in protein synthesis (YFL034C and YKL091C), and one is involved in yeast mating (YNL145W).  It does not seem likely that any of these three genes are involved in combating or causing oxidative stress because the two genes relating to protein synthesis seem to basic proteins required for the synthesis, and a yeast mating gene seems to be irrelevant.

    The combination of these three slides was not ideal especially because slide 695 contained ZMS1 mutant and the other two slides contained ZMS2 mutants. It is believed that these two genes accomplish similar functions, but to expect the same gene regulation on microarray slides with the two different mutations is not ideal. This was done to increase the amount of data, but an attempt to publish or really learn anything from this study needs further research because there is insufficient data for making any realistic conclusions. In order learn the basics of microarray analysis, combining these three slides is a reasonable idea, but it casts doubt on the conclusions made in the long run.

On Standardization

    Standardization with the mean set to zero and the standard deviation set to one is not an ideal way analyze microarray data. This type of standardization can tell you what genes are up or down regulated, but it squeezes a large amount of data into a very small group between negative one and one.  This makes determining how much a gene up or down regulated difficult to determine. For a rough estimate of up- or down-regulated genes, this type of microarray analysis may be sufficient. Should sufficient data be obtained from the microarrays, and detailed analysis take place, setting the standard deviation does not seem to be the best analysis technique.

Conclusions

    We would really like to get more data. Only working with three slides (and of questionable quality) is not enough to really have confidence that our analysis means anything, especially when one of the slides held a different mutant. More high quality slides would be required to be sure of any up- or down-regulated genes. If more slides with better data could be obtained, we would probably want to confirm the microarray results with real time PCR.