Encode Expression Data

library(tidyverse)

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SFX <- read.table('ENCFF166SFX.tsv', header = TRUE)

expression_groups <- SFX %>%
  mutate(expression_level = case_when(
    TPM == 0 ~ "Not expressed",
    TPM < 1 ~ "Low",
    TPM < 10 ~ "Moderate",
    TPM >= 10 ~ "High")) %>%
  count(expression_level)
ggplot(expression_groups, aes(x = expression_level, y = n)) +
  geom_col(fill = "pink") +
  labs(title = "Genes by Expression Level", x = "Expression Level", y = "Number of Genes") +
  theme_classic()

The bar graph identifies the genes according to their level of expression in the brain tissue. It shows that genes are expressed at different levels. Many genes have little to no expression while few genes were highly expressed. We can infer that some genes are much more active in the brain tissue, and the activity is not evenly distributed.

top20genes <- SFX %>%
  arrange(desc(TPM)) %>%
  slice_head(n = 20)
ggplot(top20genes, aes(x = reorder(gene_id, TPM), y = TPM)) +
  geom_col(fill = "orange") +
  coord_flip() +
  labs( title = "Top 20 Most Highly Expressed Genes",x = "Gene", y = "TPM") +
  theme_classic()

This plot shows the top 20 genes with the highest level of expression in the brain tissue. Highly expressed genes might be more involved in important cellular processes. This is not a clear connection between the highly expressed genes and Alzheimer’s disease, just mearly an observation based on this one brain tissue sample.

ggplot(SFX, aes(x = length, y = TPM)) +
  geom_point(shape=4, alpha = 0.3) +
  scale_y_log10() +
  labs(title = "Gene Length and Gene Expression", x = "Gene Length", y = "TPM (log scale)") + theme_classic()

## Warning in scale_y_log10(): log-10 transformation introduced infinite values.

This plot shows if gene length is related to gene expression in the brain tissue. Since the points are scattered everywhere (mainly concentrated towards the lower gene length) it is clear that gene length doesn’t drive gene expression alone. There may be other biological factors such as gene regulation or type of brain cell.