patient_microarray_data

Author

Jay V. Patankar

Published

January 29, 2025

Analysis of publicly available microarray datasets

This file analyzes the publicly available microarray datasets GSE4183 (Gyorffy et al. 2009) GSE6731 (Wu et al. 2007) GSE9686 (Carey et al. 2008) GSE10191(Ahrens et al. 2008) GSE10616 (Kugathasan et al. 2008) from IBD or infectious colitis patients and compares the expression of EGC enriched genes extracted from an integrated dataset of 1.1 million single cell transcriptomes scIBD.cn (Nie et al. 2023)

Load packages and path variables

Packages will be loaded and file paths will be defined

Code

```{r "loading required packages and path variables"}
#| code-fold: TRUE
#| warning: false
#| title: "load packages and file locations"

library(tidyverse)
library(ggrepel)
library(reticulate)
library(GEOquery)
library(limma)
library(umap)
library(AnnotationDbi)
library(org.Hs.eg.db)
```

Gyorffy et al. 2009 (GSE4183)

Code

```{r "Analyzing GSE4183"}
#| warning: false
#| title: "Standard microarray analysis workflow"
#| fig-cap: "EGC enriched gene expression in active IBD samples versus healthy"
#| fig-width: 7
#| fig-height: 5

extrafont::loadfonts(quiet = T) # important line to allow PDF font rendering

# IBD active disease versus healthy comtrols EGC comparison
source(file = "./GSE4183/GSE4183_IBDvshealthy.R")
```

EGC enriched gene expression in active IBD samples versus healthy

Wu et al. 2007 (GSE6731)

Code

```{r "Analyzing GSE6731"}
#| warning: false
#| title: "Standard scRNA Seq workflow"
#| fig-cap: "EGC enriched gene expression in active IBD samples versus healthy"
#| fig-width: 7
#| fig-height: 5

extrafont::loadfonts(quiet = T) # important line to allow PDF font rendering

# CD active vs healthy
source(file = "./GSE6731/GSE6731_healthy_CDactive_colon_analysis.R")


# Infectious vs healthy
source(file = "./GSE6731/GSE6731_healthy_Infectious_colitis_colon_analysis.R")
```

Carey et al. 2008 (GSE9686)

Code

```{r "Analyzing GSE9686"}
#| warning: false
#| title: "Standard scRNA Seq workflow"
#| fig-cap: "EGC enriched gene expression in active UC samples versus healthy"
#| fig-width: 7
#| fig-height: 5

extrafont::loadfonts(quiet = T) # important line to allow PDF font rendering


# UC vs healthy
source(file = "./GSE9686/GSE9686_UCactivevsHealthy.R")
```

EGC enriched gene expression in active UC samples versus healthy

Ahrens et al. 2008 (GSE10191)

Code

```{r "Analyzing GSE10191"}
#| warning: false
#| title: "Standard scRNA Seq workflow"
#| fig-cap: "EGC enriched gene expression in active UC samples versus healthy"
#| fig-width: 7
#| fig-height: 5

extrafont::loadfonts(quiet = T) # important line to allow PDF font rendering

# UC vs healthy
source(file = "./GSE10191/GSE10191_UCvsHealthy.R")
```

Kugathasan et al. 2008 (GSE10616)

Code

```{r "Analyzing GSE10616"}
#| warning: false
#| title: "Standard scRNA Seq workflow"
#| fig-cap: "EGC enriched gene expression in active UC samples versus healthy"
#| fig-width: 7
#| fig-height: 5

extrafont::loadfonts(quiet = T) # important line to allow PDF font rendering


# UC vs healthy
source(file = "./GSE10616/GSE10616_UCvsControl.R")
```

Export the requirements file to list out the dependencies

Code

```{r "Generating requirements.txt"}
#| results: asis

# Collect session information
session_info <- capture.output(sessionInfo())

# Get installed package details
# installed_packages <- as.data.frame(installed.packages()[, c("Package", "Version")])

# Set the file path for the requirements.txt file
requirements_file <- "requirements.txt"

# Write R version and package information to the requirements.txt file
cat(paste("R version", R.version$version.string), file = requirements_file, sep = "\n")
cat("R packages:\n", file = requirements_file, append = TRUE)

#write.table(installed_packages, file = requirements_file, append = TRUE, col.names = FALSE, row.names = FALSE, sep = " ")

# Append sessionInfo to the requirements.txt file
cat(session_info, file = requirements_file, append = TRUE, sep = "\n")

cat("Requirements file created successfully:", requirements_file, "\n")
```

Requirements file created successfully: requirements.txt

References

Ahrens, Richard, Amanda Waddell, Luqman Seidu, Carine Blanchard, Rebecca Carey, Elizabeth Forbes, Maria Lampinen, et al. 2008. “Intestinal Macrophage/Epithelial Cell-Derived CCL11/Eotaxin-1 Mediates Eosinophil Recruitment and Function in Pediatric Ulcerative Colitis.” The Journal of Immunology 181 (10): 7390–99. https://doi.org/10.4049/jimmunol.181.10.7390.

Carey, Rebecca, Ingrid Jurickova, Edgar Ballard, Erin Bonkowski, Xiaonan Han, Huan Xu, and Lee A. Denson. 2008. “Activation of an IL-6:STAT3-Dependent Transcriptome in Pediatric-Onset Inflammatory Bowel Disease.” Inflammatory Bowel Diseases 14 (4): 446–57. https://doi.org/10.1002/ibd.20342.

Gyorffy, Balazs, Bela Molnar, Hermann Lage, Zoltan Szallasi, and Aron C. Eklund. 2009. “Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples.” Edited by Chad Creighton. PLoS ONE 4 (5): e5645. https://doi.org/10.1371/journal.pone.0005645.

Kugathasan, Subra, Robert N Baldassano, Jonathan P Bradfield, Patrick M A Sleiman, Marcin Imielinski, Stephen L Guthery, Salvatore Cucchiara, et al. 2008. “Loci on 20q13 and 21q22 Are Associated with Pediatric-Onset Inflammatory Bowel Disease.” Nature Genetics 40 (10): 1211–15. https://doi.org/10.1038/ng.203.

Nie, Hu, Peilu Lin, Yu Zhang, Yihong Wan, Jiesheng Li, Chengqian Yin, and Lei Zhang. 2023. “Single-Cell Meta-Analysis of Inflammatory Bowel Disease with scIBD.” Nature Computational Science 3 (6): 522–31. https://doi.org/10.1038/s43588-023-00464-9.

Wu, Feng, Themistocles Dassopoulos, Leslie Cope, Anirban Maitra, Steven R. Brant, Mary L. Harris, Theodore M. Bayless, Giovanni Parmigiani, and Shukti Chakravarti. 2007. “Genome-Wide Gene Expression Differences in Crohn’s Disease and Ulcerative Colitis from Endoscopic Pinch Biopsies: Insights into Distinctive Pathogenesis.” Inflammatory Bowel Diseases 13 (7): 807–21. https://doi.org/10.1002/ibd.20110.