February 16, 2016
Classwork
Currently, the class is still trying to do gene ontology searches. The class is also still trying to verify organ samples and determine if any samples should be discarded as our research progresses. We also discussed in groups DEseq and learned that DEseq allows researchers to contrast two conditions and determine the differences in expression between the conditions. Ideally, when dealing with a biological experiment, conditions would be tested in replicate. Furthermore, I, personally, did not have the programming or genomics background to make sense of most of the content in the DEseq link provided by the syllabus.
Gene Search
We began our house-keeping gene search by looking through genes in the IntestineResult data in the BIO343 folder. From the Intestine Blast, interesting genes were highlighted in red and were a good starting point for genes that could help us verify the tissue samples. After identifying a gene of interest, we searched the gene in google to learn more about its function and other characteristics. The goal of our gene search is to verify all six intestine samples in order to be confident moving forward with them.
Identified Genes:
Intestine 4 fed
- Transcription factor_2 Gallus gallus
- Biological process: negative regulation of endopeptidase activity
- Belongs to the COUP transcription factor 2 group.
- Necessary for expression of chicken ovalbumin gene.
- MAKE NOTE OF WHETHER IT WAS UP OR DOWN REGULATED!
Reference Kathryn's 2/16/16 notes for a more complete list of genes to verify tissue samples.
Moving forward, after tissues are verified we want to identify transcription factors and research the genes that correlate with the identified transcription factors using supervised clustering.
