Tracking the Red & Blue: Analyzing changes in the co-expression of hypoxia-related genes over evolutionary time
By: Annie Zhang (Trinity '24)
March 2022
Research Summary
Earlier in this study, Charles identified a set of genes involved in the hypoxia response. Ones active in the regulation of the hypoxic condition in C. elegans according to publicly available gene expression data on ExpressionAtlas were then isolated. The expression levels of this subset across highly-studied species such as human, D. melanogaster, and M. musculus were recorded and a co-expression matrix constructed, accompanied by a heatmap as visual representation.
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The human matrix was then used as a means of comparison. Differential matrices between each unique species and human were created, again along with respective heatmaps, and the numbers obtained for unique gene pairs saved. Split into separate graphs by gene pair and then organized on the x-axis by species from farthest evolutionarily to human on the left and closest on the right, line graphs analyzing the change in gene expression across evolutionary time were created. P-values were calculated for each in order to determine the data's significance.
R packages used: corrplot, ggplot, ggplot2, tidyverse. To the left is an image of the human co-expression matrix.
Research Summary, cont.
To the right is an image of the ADM_BCL2 line graph with four species' worth of data (C. elegans, D. melanogaster, G. gallus differential data from human).
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Eventually, the data and visualizations created through this project will be combined with others' in the hypoxia evolution subteam for publication. Additionally, RNAseq data from cetaceans may be used to create a co-expression network, then that overlaid with the human data. Ultimately, individual species will be left out in order to study patterns amongst human-cetaceans.
