DNA Exploration

Objective

DESeq2 was used for differential gene expression analysis. This R package was used to analyze count data from RNA-Seq. Differential gene expression between Heinz 1706 apical meristem and leaf tissues will be analyzed and interpreted from DESeq2 outputs.

PCA

Analysis

This PCA plot shows statistical visualization of Euclidean distance. Here we can see that the control group (undifferentiated meristem tissues) are highly correlated and so are Leaf tissues when looking at principal component 1 which accounts for almost all of the variation. When looking at principal component 2 we still see very correlated association with Meristem tissues but we begin to see variance amongst leaf samples.

Analysis

Looking at this heat map we can see that Leaf rep 1 and Leaf rep 3 are most similar to each other amongst the leaf samples as shown by the dark shades of blue when compared to each other. This heat map also reiterates that the meristem samples are most similar to each other and so are the leaf samples.

Analysis

Here we see that as the number of counts increases there is a decrease in variation or dispersement.

Histogram of P-values for Heinz1706xtissues: meristem vs leaf

Analysis

This histogram shows the p-value of each gene being compared between meristem and leaf samples. Based on this output we have over 14000 genes that when compared have a p-value lower than the 0.05 threshold. Based on this I would recommend lowering the p-value to reduce the number of significant genes with differential gene expression and therefore determine what is really changing the most in terms of expression between the samples. I would adjust the p-value so we would get an output of about 300 genes or less lower that had significantly different expression.

Analysis

This MA-plot shows that as normalized counts increase there is more information about the difference in expression between the meristem and leaf samples.

Conclusion

Based on the DESeq2 analysis output of Heinz 1706 RNA sequencing we can see different gene expression profiles between meristem(SAM) and leaf tissues. There is a high correspondence within the two separate tissue groups and a significant difference between tissue groups.