---
title: "Week 3"
author: "Barry"
date: "4/1/2022"
output: html_document
---

## Week 3 Worksheet

Run the code block below to load the dataset containing 5 genes.

```{R, message=F, quiet=T}
library(ggpubr)
df <- read.table(url("https://raw.githubusercontent.com/BarryDigby/Youth-Academy/master/data/expr_t_n.txt"), header=T)
```

** You do not have to write code in this worksheet - the goal here is to interpret the plots and make comments on the dataset. **


## Inspecting MUC1

The MUC1 gene provides instructions for making a protein called mucin 1. This protein is one of several mucin proteins that make up mucus, a slippery substance that lubricates and protects the lining of the airways, digestive system, reproductive system, and other organs and tissues. In addition to its role in mucus, mucin 1 is involved in cell signaling and kidney development.

Run the code block below to view the distribution of MUC1 in healthy and cancer patients:

```{R}
gghistogram(df, x="MUC1", y="..count..", fill = "sample_type", add = "mean", ggtheme = theme_bw())
ggboxplot(df, x="sample_type", y="MUC1", fill = "sample_type", bxp.errorbar = T, ggtheme = theme_bw(), add = "jitter", add.params = list(alpha=0.1))
```

### Questions:

Inspect the distribution of MUC1 expression in both the histogram and boxplot (these are depicting the same information). 

1. Is there any difference between MUC1 expression in normal and tumor samples?

2. Do you think this gene is useful at distinguishing healthy vs. cancer patients? 


## Inspecting GATA3

This gene encodes a protein which belongs to the GATA family of transcription factors. These transcription factors bind to sequences of DNA containing the bases 'GATA' to initiate transcription. 

Run the code block below to view the distribution of GATA3 in healthy and cancer patients:

```{R}
gghistogram(df, x="GATA3", y="..count..", fill = "sample_type", add = "mean", ggtheme = theme_bw())
ggboxplot(df, x="sample_type", y="GATA3", fill = "sample_type", bxp.errorbar = T, ggtheme = theme_bw(), add = "jitter", add.params = list(alpha=0.1))
```

### Questions:

Inspect the distribution of GATA3 expression in both the histogram and boxplot (these are depicting the same information). 

1. Is there any difference between GATA3 expression in normal and tumor samples?

2. Do you think this gene is useful at distinguishing healthy vs. cancer patients? 


## Inspecting PTEN

PTEN is a multi-functional tumor suppressor that is very commonly lost in human cancer. Observed in prostate cancer, glioblastoma, endometrial, lung and breast cancer to varying degrees. Up to 70% of prostate cancer patients have been observed to have loss of expression of the gene.

Run the code block below to view the distribution of PTEN in healthy and cancer patients:

```{R}
gghistogram(df, x="PTEN", y="..count..", fill = "sample_type", add = "mean", ggtheme = theme_bw())
ggboxplot(df, x="sample_type", y="PTEN", fill = "sample_type", bxp.errorbar = T, ggtheme = theme_bw(), add = "jitter", add.params = list(alpha=0.1))
```

### Questions:

Inspect the distribution of PTEN expression in both the histogram and boxplot (these are depicting the same information). 

1. Is there any difference between PTEN expression in normal and tumor samples?

2. Do you think this gene is useful at distinguishing healthy vs. cancer patients? 

## Inspecting XBP1

The XBP1 gene encodes a transcription factor that regulates MHC class II genes by binding to a promoter element referred to as an X box. (This means XBP1 regulates the expression of genes involved in our immune system)

Run the code block below to view the distribution of XBP1 in healthy and cancer patients:

```{R}
gghistogram(df, x="XBP1", y="..count..", fill = "sample_type", add = "mean", ggtheme = theme_bw())
ggboxplot(df, x="sample_type", y="XBP1", fill = "sample_type", bxp.errorbar = T, ggtheme = theme_bw(), add = "jitter", add.params = list(alpha=0.1))
```

### Questions:

Inspect the distribution of XBP1 expression in both the histogram and boxplot (these are depicting the same information). 

1. Is there any difference between XBP1 expression in normal and tumor samples?

2. Do you think this gene is useful at distinguishing healthy vs. cancer patients? 

## Inspecting ESR1

The ESR1 gene regulates the transcription of many estrogen-inducible genes that play a role in growth, metabolism, sexual development, gestation, and other reproductive functions and is expressed in many non-reproductive tissues. 

Run the code block below to view the distribution of ESR1 in healthy and cancer patients:

```{R}
gghistogram(df, x="ESR1", y="..count..", fill = "sample_type", add = "mean", ggtheme = theme_bw())
ggboxplot(df, x="sample_type", y="ESR1", fill = "sample_type", bxp.errorbar = T, ggtheme = theme_bw(), add = "jitter", add.params = list(alpha=0.1))
```

### Questions:

Inspect the distribution of ESR1 expression in both the histogram and boxplot (these are depicting the same information). 

1. Is there any difference between ESR1 expression in normal and tumor samples?

2. Do you think this gene is useful at distinguishing healthy vs. cancer patients?