# 3.3 - Identifying putative probe-gene pairs

# Identifying putative probe-gene pairs

## Introduction

This step is links distal probes with methylation changes to target genes with expression changes and report the putative target gene for selected probes. This is carried out by function `get.pair`.

## Description

For each differentially methylated distal probe (DMC), the closest 10 upstream genes and the closest 10 downstream genes are tested for inverse correlation between methylation of the probe and expression of the gene, which is the same basic strategy employed in ELMER version 1. However, we now import all gene annotations programmatically using the Biomart (Durinck and others 2005) package. This allows easy extensibility to use any annotations desired (our default uses Ensembl annotations).

This step also differs between the `Supervised` and `Unsupervised` modes. In the `Unsupervised` mode, as in ELMER 1.0, for each probe-gene pair, the samples (all samples from both groups) are divided into two groups: the M group, which consist of the upper methylation quintile (the 20%of samples with the highest methylation at the enhancer probe), and the U group, which consists of the lowest methylation quintile (the 20% of samples with the lowest methylation). In the new `Supervised` mode, the U and M groups are defined strictly by sample group labels, and all samples in each group are used. For each differentially methylated distal probe (DMC), the closest 10 upstream genes and the closest 10 downstream genes are tested for inverse correlation between methylation of the probe and expression of the gene (the number 10 can be changed using the `numFlankingGenes` parameter). To select these genes, the probe-gene distance is defined as the distance from the probe to the transcription start site specified by the ENSEMBL gene level annotations (Yates and others 2015) accessed via the R/Bioconductor package biomaRt (Durinck and others 2009, @durinck2005biomart). By choosing a constant number of genes to test for each probe, our goal is to avoid systematic false positives for probes in gene rich regions. This is especially important given the highly non-uniform gene density of mammalian genomes.

Thus, exactly 20 statistical tests were performed for each probe, as follows.

For each candidate probe-gene pair, the Mann-Whitney U test is used to test the null hypothesis that overall gene expression in group M is greater than or equal than that in group U. This non-parametric test was used in order to minimize the effects of expression outliers, which can occur across a very wide dynamic range. In the `unsupervised mode` for each probe-gene pair tested, the raw p-value Pr is corrected for multiple hypothesis using a permutation approach as follows. The gene in the pair is held constant, and `x` random methylation probes are chosen to perform the same one-tailed U test, generating a set of `x` permutation p-values Pp. We chose the x random probes only from among those that were “distal” (farther than 2k b from an annotated transcription start site), in order to draw these null-model probes from the same set as the probe being tested (Sham and Purcell 2014). An empirical p-value Pe value was calculated using the following formula (which introduces a pseudo-count of 1):

In the `unsupervised mode` for each probe-gene pair tested, the raw p-value Pr is corrected for multiple hypothesis using Benjamini-Hochberg Procedure.

Notice that in the `Supervised` mode, no additional filtering is necessary to ensure that the M and U group segregate by sample group labels. The two sample groups are segregated by definition, since these probes were selected for their differential methylation, with the same directionality, between the two groups.

(Yao and others 2015)

# Function arguments

Main get.pair arguments

Argument | Description
--- | ---
data | A multiAssayExperiment with DNA methylation and Gene Expression data. See createMAE function.
nearGenes | Can be either a list containing output of GetNearGenes function or path of rda file containing output of `GetNearGenes` function.
minSubgroupFrac | A number ranging from 0 to 1.0 specifying the percentage of samples used to create groups U (unmethylated) and M (methylated) used to link probes to genes. Default is 0.4 (lowest quintile samples will be in the U group and the highest quintile samples in the M group).
permu.size | A number specify the times of permuation. Default is 10000.
raw.pvalue | A number specify the raw p-value cutoff for defining signficant pairs. Default is 0.05. It will select the significant P value cutoff before calculating the empirical p-values.
Pe | A number specify the empirical p-value cutoff for defining signficant pairs. Default is 0.001.
group.col | A column defining the groups of the sample. You can view the available columns using: `colnames(MultiAssayExperiment::colData(data))`.
group1 | A group from group.col.
group2 | A group from group.col.
mode | A character. Can be “unsupervised” or “supervised”. If unsupervised is set the U (unmethylated) and M (methylated) groups will be selected among all samples based on methylation of each probe. Otherwise U group and M group will set as the samples of group1 or group2 as described below: If diff.dir is “hypo, U will be the group 1 and M the group2. If diff.dir is”hyper" M group will be the group1 and U the group2.
diff.dir | A character can be “hypo” or “hyper”, showing differential methylation dirction in group 1. It can be “hypo” which means the probes are hypomethylated in group1; “hyper” which means the probes are hypermethylated in group1; This argument is used only when mode is supervised nad it should be the same value from get.diff.meth function.
filter.probes | Should filter probes by selecting only probes that have at least a certain number of samples below and above a certain cut-off. See `preAssociationProbeFiltering` function.
filter.portion | A number specify the cut point to define binary methlation level for probe loci. Default is 0.3. When beta value is above 0.3, the probe is methylated and vice versa. For one probe, the percentage of methylated and unmethylated samples should be above filter.percentage value. Only used if filter.probes is TRUE. See preAssociationProbeFiltering function.
filter.percentage | Minimum percentage of samples to be considered in methylated and unmethylated for the filter.portion option. Default 5%. Only used if filter.probes is TRUE. See preAssociationProbeFiltering function.

# Example of use

    # Load results from previous sections
    mae <- get(load("mae.rda"))
    sig.diff <- read.csv("result/getMethdiff.hypo.probes.significant.csv")

    nearGenes <- GetNearGenes(data = mae,
                             probes = sig.diff$probe,
                             numFlankingGenes = 20) # 10 upstream and 10 dowstream genes

    Hypo.pair <- get.pair(data = mae,
                          group.col = "definition",
                          group1 =  "Primary solid Tumor",
                          group2 = "Solid Tissue Normal",
                          nearGenes = nearGenes,
                          mode = "unsupervised",
                          permu.dir = "result/permu",
                          permu.size = 100, # Please set to 100000 to get significant results
                          raw.pvalue = 0.05,
                          Pe = 0.01, # Please set to 0.001 to get significant results
                          filter.probes = TRUE, # See preAssociationProbeFiltering function
                          filter.percentage = 0.05,
                          filter.portion = 0.3,
                          dir.out = "result",
                          cores = 1,
                          label = "hypo")

Observation: The distance column in the nearGenes object and in thable getPair.hypo.all.pairs.statistic.csv are the distance to the gene. To update, to the distance to the nearest TSS please use the function `addDistNearestTSS`. This function was not used default due to time requirements to run for all probes and all their 20 nearest genes, but it is ran for the significant pairs.

    Hypo.pair %>% datatable(options = list(scrollX = TRUE))

    # get.pair automatically save output files.
    # getPair.hypo.all.pairs.statistic.csv contains statistics for all the probe-gene pairs.
    # getPair.hypo.pairs.significant.csv contains only the significant probes which is
    # same with Hypo.pair.
    dir(path = "result", pattern = "getPair")

    ## [1] "getPair.hypo.all.pairs.statistic.csv"
    ## [2] "getPair.hypo.pairs.significant.csv"
    ## [3] "getPair.hypo.pairs.statistic.with.empirical.pvalue.csv"

# Bibliography

Durinck, Steffen, and others. 2005. “BioMart and Bioconductor: A Powerful Link Between Biological Databases and Microarray Data Analysis.” Bioinformatics 21 (16): 3439–40.

———. 2009. “Mapping Identifiers for the Integration of Genomic Datasets with the R/Bioconductor Package biomaRt.” Nature Protocols 4 (8): 1184–91.

Sham, Pak C, and Shaun M Purcell. 2014. “Statistical Power and Significance Testing in Large-Scale Genetic Studies.” Nature Reviews. Genetics 15 (5): 335.

Yao, Lijing, and others. 2015. “Inferring Regulatory Element Landscapes and Transcription Factor Networks from Cancer Methylomes.” Genome Biology 16 (1): 105.

Yates, Andrew, and others. 2015. “Ensembl 2016.” Nucleic Acids Research, gkv1157.