Introduction

We have a starting gene list of genes that are important for the immune response in monocytes and macrophages. We want to further interrogate these genes in a cell model. In this case, we have a choice between THP-1 and U937. We will use the epiChoose Shiny app to examine how these genes behave in the 2 cell lines and their relatedness to primary cell types from Blueprint.

##  [1] "JAK2"     "SH2B3"    "CD40"     "CDKN1B"   "LYN"      "CD44"    
##  [7] "STAT4"    "TRAF1"    "CDK6"     "PRKCD"    "PRKCH"    "FCGR2A"  
## [13] "CASP8"    "TYK2"     "IL2RB"    "CTLA4"    "REL"      "RIPK2"   
## [19] "LMO7"     "DDX58"    "TNFAIP3"  "IRAK1"    "IKBKG"    "IKBKE"   
## [25] "HSPA14"   "ATG5"     "PARK7"    "PTEN"     "PRDX6"    "NRG1"    
## [31] "FOXP3"    "NEDD1"    "IRF5"     "MBP"      "IL12B"    "ITGAM"   
## [37] "COL1A2"   "ITGAX"    "IFIH1"    "MAGI3"    "PTPN22"   "PRKD2"   
## [43] "FLI1"     "RUNX1"    "IRF4"     "RTKN"     "ZEB1"     "GATA3"   
## [49] "HLA-DQA1" "HLA-DRB1" "TNFSF4"   "INS"

Overview

Before starting with a specific gene list, you might want to compare the candidate cell models and the primary data across the whole genome. This can be performed under the Data Overview tab. The THP-1 and U937 cell lines were profiled as part of Project 2. Hence, we can select Project 2 from the left panel. Since THP-1 and U937 are models of primary monocytes/macrophages, we will also select Blueprint from the left panel and manually select monocytes and macrophages from the text box underneath.

After selecting the type of analysis you wish to perform (PCA or MDS), pressing Run produces multi-dimensiional scaling plots of the selected samples for each data type.

The drop-down menu at the bottom can be used to select specific data types. In this case, by selecting H3K27ac, we can see a shift towards primary cell type patterns with the addition of PMA and LPS in both THP-1 and U937: