Background

Cancer metastasis is a dynamic process in which cancer cells facilitate movement to form distant secondary tumor sites.
Epithelial-to-mesenchymal transition (EMT) is a signaled event in which non-invasive epithelial cells transition into highly invasive mesenchymal cells.
Cancer cells undergo EMT to promote cancer metastasis.

Import Packages

library(ggplot2)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(ggfortify)

Data

RNA-seq data is sourced from Cook, D.P.and Vanderhyden, B.C. Context specificity of the EMT transcriptional response. Nat Commun 11, 2142 (2020).
Analyzing two epithelial cell lines (MCF-7 and A549) which were treated with TGF-B or EGF (EMT inducers) over different amounts of time
Metadata contains information on samples including cell type, treatment type, treatment duration, and cell phase
Counts contains RNA counts of more than 13 000 different genes for each sample (only select EMT-associated genes will be analyzed)

Importing MCF-7 TGF-B Treatment Data

#MCF-7 TGF-B Metadata
meta1 <- read.csv("C:/Users/Drake/OneDrive/Graduate/Bio9915/Bio9915_Assignment/Data/GSE147405_MCF7_TGFB1_TimeCourse_metadata.csv.gz")

#MCF-7 TGF-B Counts
counts1 <- read.csv("C:/Users/Drake/OneDrive/Graduate/Bio9915/Bio9915_Assignment/Data/GSE147405_MCF7_TGFB1_TimeCourse_UMI_matrix.csv.gz")

Importing A549 TGF-B Treatment Data

#A549 TGF-B Metadata
meta2 <- read.csv("C:/Users/Drake/OneDrive/Graduate/Bio9915/Bio9915_Assignment/Data/GSE147405_A549_TGFB1_TimeCourse_metadata (1).csv.gz")

#A549 TGF-B Counts
counts2 <- read.csv("C:/Users/Drake/OneDrive/Graduate/Bio9915/Bio9915_Assignment/Data/GSE147405_A549_TGFB1_TimeCourse_UMI_matrix.csv.gz")

Importing MCF-7 EGF Treatment Data

#MCF-7 EGF Metadata
meta3 <- read.csv("C:/Users/Drake/OneDrive/Graduate/Bio9915/Bio9915_Assignment/Data/GSE147405_MCF7_EGF_TimeCourse_metadata.csv.gz")

#MCF-7 EGF Counts 
counts3 <- read.csv("C:/Users/Drake/OneDrive/Graduate/Bio9915/Bio9915_Assignment/Data/GSE147405_MCF7_EGF_TimeCourse_UMI_matrix.csv.gz")

Importing A549 EGF Treatment Data

#A549 EGF Metadata 
meta4 <- read.csv("C:/Users/Drake/OneDrive/Graduate/Bio9915/Bio9915_Assignment/Data/GSE147405_A549_EGF_TimeCourse_metadata.csv.gz")

#A549 EGF Counts
counts4 <- read.csv("C:/Users/Drake/OneDrive/Graduate/Bio9915/Bio9915_Assignment/Data/GSE147405_A549_EGF_TimeCourse_UMI_matrix.csv.gz")

Creating Single Dataset

MCF-7 TGF-B Treatment

genes   <- c("CDH1", "EPCAM", "VIM", "FN1", "SNAI1", "TGFBI")
meta_cols  <- c("CellLine", "Treatment", "Time", "Phase", "Mix")


if (!is.numeric(counts1[, 1])) 
  {rownames(counts1) <- counts1[, 1]
  counts1 <- counts1[, -1]}

genes1 <- t(counts1[genes, ])

data1 <- data.frame(
  Sample = rownames(genes1),
  meta1[, meta_cols],
  genes1,
  check.names = FALSE,
  stringsAsFactors = FALSE)

glimpse(data1)

## Rows: 1,998
## Columns: 12
## $ Sample    <chr> "Mix1_AAACCTGTCGCTTGTC", "Mix1_AAACCTGTCTATCGCC", "Mix1_AAAG…
## $ CellLine  <chr> "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF…
## $ Treatment <chr> "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1…
## $ Time      <chr> "8h", "3d", "0d", "1d", "3d", "0d", "8h_rm", "0d", "1d", "8h…
## $ Phase     <chr> "S", "G1", "S", "G1", "G2M", "S", "S", "G2M", "G1", "G1", "G…
## $ Mix       <chr> "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix…
## $ CDH1      <int> 0, 1, 1, 2, 1, 1, 1, 3, 6, 3, 0, 2, 7, 1, 1, 3, 3, 2, 1, 4, …
## $ EPCAM     <int> 6, 1, 5, 2, 3, 4, 2, 1, 2, 2, 2, 2, 3, 3, 2, 1, 4, 2, 5, 0, …
## $ VIM       <int> 0, 0, 0, 1, 1, 0, 0, 0, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, …
## $ FN1       <int> 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 2, 0, 0, 1, 0, 0, 0, 0, …
## $ SNAI1     <int> 1, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ TGFBI     <int> 0, 0, 0, 1, 0, 0, 0, 0, 0, 2, 0, 0, 0, 1, 3, 0, 0, 0, 1, 0, …

A549 TGF-B Treatment

if (!is.numeric(counts2[, 1])) 
  {rownames(counts2) <- counts2[, 1]
  counts2 <- counts2[, -1]}

genes2 <- t(counts2[genes, ])

data2 <- data.frame(
  Sample = rownames(genes2),
  meta2[, meta_cols],
  genes2,
  check.names = FALSE,
  stringsAsFactors = FALSE)

glimpse(data2)

## Rows: 3,568
## Columns: 12
## $ Sample    <chr> "Mix1_AAAGCAACACTTCGAA", "Mix1_AACTCTTCACAGCCCA", "Mix1_AAGC…
## $ CellLine  <chr> "A549", "A549", "A549", "A549", "A549", "A549", "A549", "A54…
## $ Treatment <chr> "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1…
## $ Time      <chr> "3d", "3d", "3d", "3d", "3d", "7d", "3d", "1d", "7d", "3d", …
## $ Phase     <chr> "S", "G2M", "S", "G1", "S", "G1", "G2M", "G1", "G1", "G1", "…
## $ Mix       <chr> "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix…
## $ CDH1      <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ EPCAM     <int> 1, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, 0, 1, 0, 0, 0, 0, 2, 0, 0, …
## $ VIM       <int> 23, 25, 67, 31, 25, 22, 9, 47, 48, 7, 36, 29, 4, 14, 42, 29,…
## $ FN1       <int> 1, 1, 4, 5, 4, 1, 0, 1, 1, 11, 3, 0, 6, 1, 1, 1, 1, 1, 2, 2,…
## $ SNAI1     <int> 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, …
## $ TGFBI     <int> 27, 29, 69, 38, 13, 16, 17, 21, 16, 22, 25, 18, 12, 8, 23, 3…

MCF-7 EGF Treatment

if (!is.numeric(counts3[, 1])) 
  {rownames(counts3) <- counts3[, 1]
  counts3 <- counts3[, -1]}

genes3 <- t(counts3[genes, ])

data3 <- data.frame(
  Sample = rownames(genes3),
  meta3[, meta_cols],
  genes3,
  check.names = FALSE,
  stringsAsFactors = FALSE)

glimpse(data3)

## Rows: 3,177
## Columns: 12
## $ Sample    <chr> "Mix1_AAACGGGGTGGCAAAC", "Mix1_AAACGGGGTTCGAATC", "Mix1_AAAG…
## $ CellLine  <chr> "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF…
## $ Treatment <chr> "EGF", "EGF", "EGF", "EGF", "EGF", "EGF", "EGF", "EGF", "EGF…
## $ Time      <chr> "1d", "3d_rm", "8h", "3d_rm", "1d_rm", "0d", "0d", "1d", "1d…
## $ Phase     <chr> "G2M", "G1", "G1", "G1", "G1", "G1", "G1", "S", "G1", "G1", …
## $ Mix       <chr> "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix…
## $ CDH1      <int> 0, 0, 3, 1, 1, 1, 4, 3, 6, 3, 1, 1, 0, 7, 2, 1, 0, 1, 1, 1, …
## $ EPCAM     <int> 1, 3, 5, 4, 5, 2, 4, 7, 1, 5, 5, 0, 2, 2, 1, 3, 2, 1, 3, 6, …
## $ VIM       <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 2, 0, 0, …
## $ FN1       <int> 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 2, 0, 1, 0, 0, 0, 0, 0, 0, …
## $ SNAI1     <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, …
## $ TGFBI     <int> 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, …

A549 EGF Treatment

if (!is.numeric(counts4[, 1])) 
  {rownames(counts4) <- counts4[, 1]
  counts4 <- counts4[, -1]}

genes4 <- t(counts4[genes, ])

data4 <- data.frame(
  Sample = rownames(genes4),
  meta4[, meta_cols],
  genes4,
  check.names = FALSE,
  stringsAsFactors = FALSE)

glimpse(data4)

## Rows: 12,435
## Columns: 12
## $ Sample    <chr> "Mix1_AAACCTGAGGATGGAA", "Mix1_AAACCTGTCTATCCTA", "Mix1_AAAC…
## $ CellLine  <chr> "A549", "A549", "A549", "A549", "A549", "A549", "A549", "A54…
## $ Treatment <chr> "EGF", "EGF", "EGF", "EGF", "EGF", "EGF", "EGF", "EGF", "EGF…
## $ Time      <chr> "3d", "8h_rm", "7d", "8h_rm", "0d", "1d", "7d", "3d", "3d", …
## $ Phase     <chr> "S", "G1", "G1", "G2M", "G1", "S", "S", "S", "S", "G1", "G1"…
## $ Mix       <chr> "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix…
## $ CDH1      <int> 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ EPCAM     <int> 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ VIM       <int> 12, 2, 3, 13, 10, 21, 16, 10, 10, 11, 15, 11, 11, 3, 11, 5, …
## $ FN1       <int> 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ SNAI1     <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ TGFBI     <int> 2, 1, 0, 3, 2, 2, 1, 1, 1, 2, 0, 3, 0, 0, 1, 1, 1, 4, 4, 4, …

Final Step

master_data <- rbind(data1, data2, data3, data4)
rownames(master_data) <- NULL

glimpse(master_data)

## Rows: 21,178
## Columns: 12
## $ Sample    <chr> "Mix1_AAACCTGTCGCTTGTC", "Mix1_AAACCTGTCTATCGCC", "Mix1_AAAG…
## $ CellLine  <chr> "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF7", "MCF…
## $ Treatment <chr> "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1", "TGFB1…
## $ Time      <chr> "8h", "3d", "0d", "1d", "3d", "0d", "8h_rm", "0d", "1d", "8h…
## $ Phase     <chr> "S", "G1", "S", "G1", "G2M", "S", "S", "G2M", "G1", "G1", "G…
## $ Mix       <chr> "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix1", "Mix…
## $ CDH1      <int> 0, 1, 1, 2, 1, 1, 1, 3, 6, 3, 0, 2, 7, 1, 1, 3, 3, 2, 1, 4, …
## $ EPCAM     <int> 6, 1, 5, 2, 3, 4, 2, 1, 2, 2, 2, 2, 3, 3, 2, 1, 4, 2, 5, 0, …
## $ VIM       <int> 0, 0, 0, 1, 1, 0, 0, 0, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, …
## $ FN1       <int> 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 2, 0, 0, 1, 0, 0, 0, 0, …
## $ SNAI1     <int> 1, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ TGFBI     <int> 0, 0, 0, 1, 0, 0, 0, 0, 0, 2, 0, 0, 0, 1, 3, 0, 0, 0, 1, 0, …

Bio9915_Assignment

Vink

11/2/2026

Background

Import Packages

Data

Importing MCF-7 TGF-B Treatment Data

Importing A549 TGF-B Treatment Data

Importing MCF-7 EGF Treatment Data

Importing A549 EGF Treatment Data

Creating Single Dataset

MCF-7 TGF-B Treatment

A549 TGF-B Treatment

MCF-7 EGF Treatment

A549 EGF Treatment

Final Step