Ovarian Cancer Meta Analysis Validation - Forest Plots

Genes reported by Yip et al., 2011 in prospective study looking for potential serum biomarkers

What did these genes look like in my meta-analysis datasets?

Yip et al. 2011 did prospective screen to find novel biomarkers. Top 9 evaluated in detail in paper, here I show how the top 20 look in our meta-analysis.

PRSS8 is in our list of top 80, MMP7 and MUC16 are on the top 160 list but not upregulated in early stage TCGA cohort

setwd("/Users/lszabo/Documents/RProjects/ButteLab/biomarkers")
source("forestplot.R")

## Loading required package: rmeta

## Loading required package: grid

load("Ovarian_Cancer_Analysis.RData")  #all data objects from meta-analysis

# gene 8: CA-72-4 - couldn't figure out what gene this is
yip_genes <- c("WFDC2", "MUC16", "IL2RA", "SERPINA1", "CRP", "CHI3L1", "FN1", 
    "PRSS8", "TIMP1", "IL8", "MMP7", "IL7", "VEGFB", "S100A9", "S100A8", "IGFBP2", 
    "OLR1", "NRP1", "TNFRSF1B", "CCL23")

for (i in 1:length(yip_genes)) {
    forest.plot(allData$output.REM, key = yip_genes[i])
}

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First needed to find which TNFR2 synonym was used in our meta-analysis.

valid.synonym(allData$output.REM, "TNFR2")

## Loading required package: DBI

## Loading required package: RMySQL

## [1] "TNFRSF1B"