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Using the `target` package
In target: Predict Combined Function of Transcription Factors
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Overview
In this document, we describe the BETA algorithm
for predicting associated peaks from binding ChIP data and integrating binding
data and expression data to predict direct binding target regions. In addition,
we describe the implementation of the algorithm in an R package, target.
Finally, we provide an example for using target to predict associated peaks
and direct gene targets of androgen receptors in the LNCap cell line.
The theory
The BETA algorithm in its simplest form, minus,
is composed of three steps:
- Selecting the peaks ($p$) within a certain range from the regions of
interest ($g$).
- Calculate the distance ($\Delta$) between the center of the peak and each
of the regions expressed relative to a distance of 100 kb.
- Calculate a the peak scores ($S_p$) as the transformed exponential of the
distance, $\Delta$, as follows;
$$
S_p = e^{-(0.5+4\Delta)}
$$
- Calculate the region/gene regulatory potential ($S_g$) as the sum of the
scores, $S_p$, as follows:
$$
S_g = \sum_{i=1}^k S_{pi}
$$
where $p$ is ${1,...,k}$ peaks near the region of interest.
In addition, in BETA basic another step is added
to predict real region/gene targets
- Rank all regions based on their regulatory potential, $S_g$, to give their
binding potential ($R_{gb}$) and based on their differential expression
($R_{ge}$). The product of the two ranks predicts real region/gene targets.
$$
RP_g = \frac{R_{gb}\times R_{ge}}{n^2}
$$
where $n$ is the number of regions $g$.
Python implementation
The original paper on
this work presented an implementation of the algorithm in
python which can be invoked form the
command-line interface (CLI).
-
Input: peaks file in bed format and optionally the differential expression
output in txt
-
Output: txt files of the associated peaks and direct targets in each
direction; up and/or down.
-
Options: users can define the distances around the transcription start sites
to select the overlapping peaks, cut offs for the significance of the peaks or
the top number of peaks to be included in the analysis.
R implementation
The target package implement the BETA algorithm
in several low-level functions that correspond to the previously described
steps.
merge_ranges: select the peaks in the genomic regions of interest, e.g.
genes.find_distance: calculate the distance between the peaks and the regions
of interest, e.g. transcription start sites (TSS).score_peaks: calculate a regulatory score for each peak in relation to a
region of interest.score_regions: Calculate a regulatory score for regions of interest/genesrank_product: rank the regions of interest/genes based on the regulatory
potential and another statistics, e.g. differential expression.
In addition, two high-level functions can be used to apply these functions
sequentially and obtain only the final output. These are:
associated_peaks: select and calculate a regulatory potential for peaks
within a defined distance from regions of interest/genes.direct_targets: predict direct target regions among regions of
interest/genes based on the regulatory potential of the peaks in the region
and one more statistics such as differential expression.
Finally, two additional functions plot_predictions and test_predictions
were added to visually and statistically examine the predictions made by
target.
Example
The example below was presented in this
paper. The dataset
used in the example is from another published
study. The study used the
LNCap cell line to determine the androgen receptor (AR) binding sites using
ChIP-on-chip and the gene expression in the cell line after treatment with
physiological androgen 5α-dihydrotestosterone (DHT) for 16 hours using
microarrays. The binding sites of AR are recorded in a bed file,
3656_peaks.bed. The differential gene expression results are recorded in
AR_diff_expr.xls. The reference genome
hg19 was used to
define the gene coordinates and identifiers, hg19.refseq.
# load reguired libraries
library(target)
library(GenomicRanges)
Each of the three following chuncks is reading one of the required input data
and transforming it into the appropriate format. The test data of the
python package is shipped with the R
target package for testing purposes. Two datasets real_peaks and
real_transcripts are the two GRanges object that holds the identified peaks
and the differential expression results respectively.
# load peaks and transcripts data
data("real_peaks")
data("real_transcripts")
The two high-level functions mentioned above can be called directly into the
objects. associated_peaks takes as arguments two GRanges objects; peaks
and regions. In this case, the two inputs are the peaks and transcripts
which we prepared earlier. The output of this function is a GRanges, the
same as the input peaks, with three additional metadata columns:
assigned_region, distance and peak_score.
# get associated peaks
ap <- associated_peaks(real_peaks, real_transcripts, 'ID')
ap
direct_targets also takes as arguments two GRanges objects; peaks and
regions. Two other arguments are required when the user desires to rank the
target genes based on both the regulatory potential and the differential
expression statistics. The arguments are regions_col and stats_col, these
should be strings for the columns names in the metadata of the regions
object for the gene names/symbols and the chosen statistics to rank the genes.
The output of this function is a GRanges, the same as the input regions,
with four additional metadata columns: score, stat, score_rank,
stat_rank and rank. These correspond to the regulatory potential gene
score, the chosen statistics, the rank of each and the final rank product.
The values in the rank column are the product of the two ranks, the less
the value the more likely a region/gene is a direct target. The direction of
the regulation can be infered from the sign of the stat column.
# get direct targets
dt <- direct_targets(real_peaks, real_transcripts, 'ID', 't')
dt
The following code shows the relation between the peak distance and the peak
score (left), the genes t-statitics and the gene regulatory potentials
(middle), and the emperical cumlative distribution function (ECDF) of the
regulatory potential ranks of the up, down and non-regulated genes (right) .
par(mfrow = c(1, 3))
# show peak distance vs score
plot(ap$distance, ap$peak_score,
pch = 19, cex = .5,
xlab = 'Peak Distance', ylab = 'Peak Score')
abline(v = 0, lty = 2, col = 'gray')
# show gene stat vs score
plot(dt$stat, dt$score,
pch = 19, cex = .5,
xlim = c(-35, 35),
xlab = 'Gene t-stats', ylab = 'Gene Score')
abline(v = 0, lty = 2, col = 'gray')
# show gene regulatory potential ecdf
groups <- c('Down', 'None', 'Up')
colors <- c('darkgreen', 'gray', 'darkred')
fold_change <- cut(dt$logFC,
breaks = c(min(dt$logFC), -.5, .5, max(dt$logFC)),
labels = groups)
plot_predictions(dt$score_rank,
fold_change,
colors,
groups,
xlab = 'Gene Regulatory Potential Rank',
ylab = 'ECDF')
The graph shows that more of the up-regulated transcripts are ranking higher
than the down- and none-regulated genes. We can test whether the distribution
function of the two regulated group are drawn from the same distribution of
the none-regulated transcripts.
# test up-regulated transcripts are not random
test_predictions(dt$score_rank,
group = fold_change,
compare = c('Up', 'None'),
alternative = 'greater')
# test down-regulated transcripts are not random
test_predictions(dt$score_rank,
group = fold_change,
compare = c('Down', 'None'),
alternative = 'greater')
The names of the top regulated transcript by rank, gene name and its associated
peaks.
# show the top regulated transcript, gene name and its associated peaks
top_trans <- unique(dt$ID[dt$rank == min(dt$rank)])
top_trans
unique(dt$name2[dt$ID == top_trans])
unique(ap$peak_name[ap$assigned_region == top_trans])
Advantages of the R implementation
The target package implements the BETA algorithm
for detecting the associated peaks of DNA-binding proteins or histone markers
from ChIP data. In addition, when genetic or chemical perturbation data is
provided the algorithm can predict direct target regions of the protein or the
marker by integrating the binding and the expression data. The implementation of
the algorithm in R provide a few advantages:
-
target leverages the Bioconductor data structures such as GRanges and
DataFrame to provide flexible containers which can be manipulated and updated
to prepare the input data. The containers are also faster to perform merge and
selection operations on.
-
In the R package, the input data are limited to the peaks and the regions
expression data. This gives the users more control. For example, regions can
be defined as genes, transcripts, promoters of differentially expressed
regions. Similarly, the expression data can be any signed statistics that
corresponds to the defined regions. Finally, any old or recent can be used
to define genomic coordinates without being limited to built in reference
genomes.
-
The same R functions can be used to predict the combined function of two
factors in the same condition. Predicting cooperative or competitive effect
of two factors is described in vignette('extend-target').
References
Wang S, Sun H, Ma J, et al. Target analysis by integration of transcriptome and
ChIP-seq data with BETA. Nat Protoc. 2013;8(12):2502–2515.
doi:10.1038/nprot.2013.150
Wang Q, Li W, Liu XS, et al. A hierarchical network of transcription factors
governs androgen receptor-dependent prostate cancer growth. Mol Cell.
2007;27(3):380–392. doi:10.1016/j.molcel.2007.05.041
sessionInfo()
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knitr::opts_chunk$set( collapse = TRUE, comment = "#>", message = FALSE, warning = FALSE )
Overview
In this document, we describe the BETA algorithm
for predicting associated peaks from binding ChIP data and integrating binding
data and expression data to predict direct binding target regions. In addition,
we describe the implementation of the algorithm in an R package, target.
Finally, we provide an example for using target to predict associated peaks
and direct gene targets of androgen receptors in the LNCap cell line.
The theory
The BETA algorithm in its simplest form, minus, is composed of three steps:
- Selecting the peaks ($p$) within a certain range from the regions of interest ($g$).
- Calculate the distance ($\Delta$) between the center of the peak and each of the regions expressed relative to a distance of 100 kb.
- Calculate a the peak scores ($S_p$) as the transformed exponential of the distance, $\Delta$, as follows;
$$ S_p = e^{-(0.5+4\Delta)} $$
- Calculate the region/gene regulatory potential ($S_g$) as the sum of the scores, $S_p$, as follows:
$$ S_g = \sum_{i=1}^k S_{pi} $$ where $p$ is ${1,...,k}$ peaks near the region of interest.
In addition, in BETA basic another step is added to predict real region/gene targets
- Rank all regions based on their regulatory potential, $S_g$, to give their binding potential ($R_{gb}$) and based on their differential expression ($R_{ge}$). The product of the two ranks predicts real region/gene targets.
$$ RP_g = \frac{R_{gb}\times R_{ge}}{n^2} $$
where $n$ is the number of regions $g$.
Python implementation
The original paper on this work presented an implementation of the algorithm in python which can be invoked form the command-line interface (CLI).
-
Input: peaks file in
bedformat and optionally the differential expression output intxt -
Output:
txtfiles of the associated peaks and direct targets in each direction; up and/or down. -
Options: users can define the distances around the transcription start sites to select the overlapping peaks, cut offs for the significance of the peaks or the top number of peaks to be included in the analysis.
R implementation
The target package implement the BETA algorithm
in several low-level functions that correspond to the previously described
steps.
merge_ranges: select the peaks in the genomic regions of interest, e.g. genes.find_distance: calculate the distance between the peaks and the regions of interest, e.g. transcription start sites (TSS).score_peaks: calculate a regulatory score for each peak in relation to a region of interest.score_regions: Calculate a regulatory score for regions of interest/genesrank_product: rank the regions of interest/genes based on the regulatory potential and another statistics, e.g. differential expression.
In addition, two high-level functions can be used to apply these functions sequentially and obtain only the final output. These are:
associated_peaks: select and calculate a regulatory potential for peaks within a defined distance from regions of interest/genes.direct_targets: predict direct target regions among regions of interest/genes based on the regulatory potential of the peaks in the region and one more statistics such as differential expression.
Finally, two additional functions plot_predictions and test_predictions
were added to visually and statistically examine the predictions made by
target.
Example
The example below was presented in this
paper. The dataset
used in the example is from another published
study. The study used the
LNCap cell line to determine the androgen receptor (AR) binding sites using
ChIP-on-chip and the gene expression in the cell line after treatment with
physiological androgen 5α-dihydrotestosterone (DHT) for 16 hours using
microarrays. The binding sites of AR are recorded in a bed file,
3656_peaks.bed. The differential gene expression results are recorded in
AR_diff_expr.xls. The reference genome
hg19 was used to
define the gene coordinates and identifiers, hg19.refseq.
# load reguired libraries library(target) library(GenomicRanges)
Each of the three following chuncks is reading one of the required input data
and transforming it into the appropriate format. The test data of the
python package is shipped with the R
target package for testing purposes. Two datasets real_peaks and
real_transcripts are the two GRanges object that holds the identified peaks
and the differential expression results respectively.
# load peaks and transcripts data data("real_peaks") data("real_transcripts")
The two high-level functions mentioned above can be called directly into the
objects. associated_peaks takes as arguments two GRanges objects; peaks
and regions. In this case, the two inputs are the peaks and transcripts
which we prepared earlier. The output of this function is a GRanges, the
same as the input peaks, with three additional metadata columns:
assigned_region, distance and peak_score.
# get associated peaks ap <- associated_peaks(real_peaks, real_transcripts, 'ID') ap
direct_targets also takes as arguments two GRanges objects; peaks and
regions. Two other arguments are required when the user desires to rank the
target genes based on both the regulatory potential and the differential
expression statistics. The arguments are regions_col and stats_col, these
should be strings for the columns names in the metadata of the regions
object for the gene names/symbols and the chosen statistics to rank the genes.
The output of this function is a GRanges, the same as the input regions,
with four additional metadata columns: score, stat, score_rank,
stat_rank and rank. These correspond to the regulatory potential gene
score, the chosen statistics, the rank of each and the final rank product.
The values in the rank column are the product of the two ranks, the less
the value the more likely a region/gene is a direct target. The direction of
the regulation can be infered from the sign of the stat column.
# get direct targets dt <- direct_targets(real_peaks, real_transcripts, 'ID', 't') dt
The following code shows the relation between the peak distance and the peak score (left), the genes t-statitics and the gene regulatory potentials (middle), and the emperical cumlative distribution function (ECDF) of the regulatory potential ranks of the up, down and non-regulated genes (right) .
par(mfrow = c(1, 3)) # show peak distance vs score plot(ap$distance, ap$peak_score, pch = 19, cex = .5, xlab = 'Peak Distance', ylab = 'Peak Score') abline(v = 0, lty = 2, col = 'gray') # show gene stat vs score plot(dt$stat, dt$score, pch = 19, cex = .5, xlim = c(-35, 35), xlab = 'Gene t-stats', ylab = 'Gene Score') abline(v = 0, lty = 2, col = 'gray') # show gene regulatory potential ecdf groups <- c('Down', 'None', 'Up') colors <- c('darkgreen', 'gray', 'darkred') fold_change <- cut(dt$logFC, breaks = c(min(dt$logFC), -.5, .5, max(dt$logFC)), labels = groups) plot_predictions(dt$score_rank, fold_change, colors, groups, xlab = 'Gene Regulatory Potential Rank', ylab = 'ECDF')
The graph shows that more of the up-regulated transcripts are ranking higher than the down- and none-regulated genes. We can test whether the distribution function of the two regulated group are drawn from the same distribution of the none-regulated transcripts.
# test up-regulated transcripts are not random test_predictions(dt$score_rank, group = fold_change, compare = c('Up', 'None'), alternative = 'greater') # test down-regulated transcripts are not random test_predictions(dt$score_rank, group = fold_change, compare = c('Down', 'None'), alternative = 'greater')
The names of the top regulated transcript by rank, gene name and its associated peaks.
# show the top regulated transcript, gene name and its associated peaks top_trans <- unique(dt$ID[dt$rank == min(dt$rank)]) top_trans unique(dt$name2[dt$ID == top_trans]) unique(ap$peak_name[ap$assigned_region == top_trans])
Advantages of the R implementation
The target package implements the BETA algorithm
for detecting the associated peaks of DNA-binding proteins or histone markers
from ChIP data. In addition, when genetic or chemical perturbation data is
provided the algorithm can predict direct target regions of the protein or the
marker by integrating the binding and the expression data. The implementation of
the algorithm in R provide a few advantages:
-
targetleverages the Bioconductor data structures such asGRangesandDataFrameto provide flexible containers which can be manipulated and updated to prepare the input data. The containers are also faster to perform merge and selection operations on. -
In the R package, the input data are limited to the peaks and the regions expression data. This gives the users more control. For example, regions can be defined as genes, transcripts, promoters of differentially expressed regions. Similarly, the expression data can be any signed statistics that corresponds to the defined regions. Finally, any old or recent can be used to define genomic coordinates without being limited to built in reference genomes.
-
The same R functions can be used to predict the combined function of two factors in the same condition. Predicting cooperative or competitive effect of two factors is described in
vignette('extend-target').
References
Wang S, Sun H, Ma J, et al. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc. 2013;8(12):2502–2515. doi:10.1038/nprot.2013.150
Wang Q, Li W, Liu XS, et al. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell. 2007;27(3):380–392. doi:10.1016/j.molcel.2007.05.041
sessionInfo()
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Any scripts or data that you put into this service are public.
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