Ellen Brooks/Dr. Robert Marx - Week 3

 Dr. Marx was out of town this week, so I focused my time in laboratory work.

In the lab, I am looking at the changes in genetic pathways that are active in cartilage 24 hours after impacting. The data show that there are 11 pathways that are significantly altered following impact (p<0.05). These pathways are associated with inflammation, bone and cartilage maintenance, and mitochondrial function. 

In the plot below, each circle represents a significantly altered genetic pathway. The size of the circle shows how many genes are in each pathway, the color indicates the p-value, and the position above or below the axis indicates how much that pathway was altered with impact. 

I have started to compare this data to several other data sets with the goal of determining which genetic pathways are uniquely altered in impact as compared to other treatments. One of these data sets looks at the impact of IL-1B treatment. IL-1B is important in regulating the innate immune system and inflammatory responses. Comparing the data of IL-1B treated to impacted cartilage shows that 8 of the pathways overlap, but three pathways were uniquely found in the impact data set. These unique pathways may help determine what is happening in cartilage in response to impact and this knowledge may assist in future treatments for damaged cartilage. 

In addition to pathways, I also looked at significantly altered individual genes in the data set. The following plot shows, in blue, individual genes that are significantly altered with impact and in a pathway that is significantly altered with impact. 

Throughout the summer, I will continue working with Dr. Chen and Dr. Singh on this data set. 

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