Package `GSCA`

Package ‘GSCA’
December 15, 2015
Type Package
Title GSCA: Gene Set Context Analysis
Version 1.8.0
Date 2015-1-6
Author Zhicheng Ji, Hongkai Ji
Maintainer Zhicheng Ji <zji4@jhu.edu>
Description GSCA takes as input several lists of activated and
repressed genes. GSCA then searches through a compendium of
publicly available gene expression profiles for biological
contexts that are enriched with a specified pattern of gene
expression. GSCA provides both traditional R functions and
interactive, user-friendly user interface.
License GPL(>=2)
LazyLoad yes
Imports graphics
Depends shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5,
R(>= 2.10.0)
Suggests Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr,
Affyhgu133Plus2Expr
biocViews GeneExpression, Visualization, GUI
NeedsCompilation no
R topics documented:
GSCA-package
annotatePeaks .
ConstructTG .
geneIDdata . .
GSCA . . . . .
GSCAeda . . .
GSCAplot . . .
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2
GSCA-package
GSCAui . . .
Oct4ESC_TG
STAT1_TG .
tabSearch . .
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Index
GSCA-package
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14
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GSCA: Gene Set Context Analysis
Description
GSCA analyzes biological contexts enriched within given patterns of geneset expression activity.
GSCA takes as input several lists of activated and repressed genes. Though the input genesets could
contain any gene which interest users, they are usually dervied from ChIP-chip or ChIP-seq (ChIPx)
and gene expression data in one or more biological systems, for example TF target genes (genes
that are both TF-bound in the ChIPx data and differentially expressed in the gene expression data).
Then GSCA uses the given genesets to scan through a compendium of gene expression profiles
constructed from publicly available gene expression data to search for patterns of geneset expression
activity specified by the users. The final output of GSCA is a ranked table of biological contexts
that are significantly enriched with the specified pattern of geneset expression activity. After the
initial GSCA analysis, users can further study the predicted biological contexts and related contexts
in more detail using the tabSearch function to search for contexts of interest in the human or mouse
compendium, and the GSCAeda function to visualize and test for differences in geneset expression
activities of the recovered contexts. Further functions to help annotate peaks and construct TF target
genes are also provided if users are interested in exploring enriched biological contexts in given TF
expression and target gene activity. Besides traditional R functions, GSCA also provides a userfriendly interactive user interface based on R shiny. Users can run GSCAui function to run the UI
in the web browser on their own computer (need to install shiny and GSCAdata package) or go to
http://spark.rstudio.com/jzc19900805/GSCA/ to run the UI on shiny server (only a web browser is
required, do not need to install GSCA, GSCAdata or R).
Details
Package:
Type:
Version:
Date:
License:
GSCA
Package
0.99.1
2014-2-9
GPL-2
Author(s)
Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji <zji4@jhu.edu>
annotatePeaks
3
References
George Wu, et al. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics
2013 Apr 23;29(9):1182-1189.
annotatePeaks
Annotate ChIPx peaks with genes by Entrez GeneIDs
Description
This function finds all genes that overlap with each peak detected from TF ChIP-chip or ChIP-seq
data. Assigned genes are assumed to be genes bound by the TF.
Usage
annotatePeaks(inputfile, genome, up = NULL, down = NULL)
Arguments
inputfile
A data.frame where each row corresponds to a peak. The first column is the
chromosome on which the peak is found (e.g., chr1) and the second and third
columns are the peak starting and ending sites.
genome
Should be one of ’hg19’, ’hg18’, ’mm9’, or ’mm8’ genome. More genomes
may be supported in future versions of GSCA.
up
Region upstream of the TSS. A gene will be annotated to a peak if the region
upstream to downstream of each gene TSS, as defined by the up and down arguments, overlap with the peak.
down
Region downstream of the TSS. A gene will be annotated to a peak if the region upstream to downstream of each gene TSS, as defined by the up and down
arguments, overlap with the peak.
Details
A gene will be annotated to a peak if the region upstream to downstream of each gene TSS, as
defined by the up and down arguments, overlap with the peak.
Value
Returns a data.frame with the same columns as the input data.frame and an additional column
containing the Enterz GeneIDs for all genes that overlap with the peak. Multiple genes will be
separated with ’;’ and ’-9’ will be reported if no genes are found.
Author(s)
Zhicheng Ji, Hongkai Ji
4
ConstructTG
References
Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core
transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17.
George Wu, et al. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics
2013 Apr 23;29(9):1182-1189.
Examples
### Read in example ChIP-seq analyzed data output from GSE11431
### for Oct4 in ESCs directly downloaded from NCBI GEO
path <- system.file("extdata",package="GSCA")
inputfile <- read.delim(paste(path,"GSM288346_ES_Oct4.txt",sep="/"), header=FALSE,stringsAsFactors=FALSE)
### Note that 1st column is chr, 2nd and 3rd columns are starting and ending sites of peaks
### Remaining columns are other output from the peak detection algorithm
head(inputfile)
### annotatePeaks only requires the first 3 columns
annon.out <- annotatePeaks(inputfile,"mm8",10000,5000)
head(annon.out)
ConstructTG
Construct target genes for a TF using TF-bound genes and differentially expressed genes from ChIP-chip or ChIP-seq and TF perturbation gene expression data.
Description
This function requires users to first analyze their own ChIP-chip and ChIP-seq data to detect significant peaks and then annotate the peaks with their corresponding regulated target genes using the
annotatePeaks function in the GSCA package. Users must also use the limma package to detect
differentially expressed genes in their gene expression data (preprocessing and noramzliation can
be done with any algorithm the user desires), then the resulting output needs to be annotated into
Entrez GeneIDs. Finally, with both inputs ConstructTG will identify the activated and repressed TF
target genes.
Usage
ConstructTG(annonPeaksOut, limmaOut)
Arguments
annonPeaksOut
Output from the annotatePeaks function in the GSCA package. Contains the
genes that correspond to the significant peaks detected from TF ChIP-chip or
ChIP-seq data.
limmaOut
Differential expression output from the limma package, and requires the first
column of the data.frame to contain the EntrezGeneIDs that match the microarray probeset IDs.
ConstructTG
5
Details
This function is designed as one method to allow users to construct target genes after obtaining a
list of significant peaks from ChIP-chip or ChIP-seq data and differential expression results from
using limma to anaylze their microarray data. It is not designed to be flexible to account for all
methods to obtain TF-bound and/or differentially expressed genes. Users can choose to manually
intersect their own TF-bound and differentially expressed genes by classifying activated genes as
genes, whose expression increases when the TF expression increases and repressed genes as genes,
who expression decreases when the TF expression increases. Note, that significant cutoffs for peaks
and differentially expressed genes need to be already applied prior to input.
Value
Returns a list with two items:
PosTG
Activated TF target genes
NegTG
Repressed TF target genes
Author(s)
Zhicheng Ji, Hongkai Ji
References
George Wu, et al. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics
2013 Apr 23;29(9):1182-1189.
Examples
### Read in example ChIP-seq analyzed data output from GSE11431
### for Oct4 in ESCs directly downloaded from NCBI GEO
path <- system.file("extdata",package="GSCA")
chipxfile <- read.delim(paste(path,"GSM288346_ES_Oct4.txt",sep="/"),
header=FALSE,stringsAsFactors=FALSE)
### annotate each peak with the corresponding gene target
annon.out <- annotatePeaks(chipxfile,"mm8",10000,5000)
### Read in example limma output from gene expression data obtained
### by analyzing Oct4 RNAi knockdown gene with RMA then limma
### from the raw CEL files in GSE4189
### The first column contains the Entrez GeneID for each probeset ID
### annotated using the mouse4302.db package in Bioconductor.
gp.out <- read.delim(paste(path,"Pou5f1_E14TG2a_GSE4189_Limma.txt",sep="/"),
stringsAsFactors=FALSE)
ConstructTG(annon.out,gp.out)
6
GSCA
geneIDdata
Homologene data
Description
Homologene data to support conversion of ENTREZ gene ID and gene name between human and
mouse species.
References
http://www.ncbi.nlm.nih.gov/homologene
Examples
data(geneIDdata)
GSCA
GSCA
Description
The function takes as input several lists of activated and repressed genes. It then searches through a
compendium of publicly available gene expression profiles for biological contexts that are enriched
with a specified pattern of gene expression.
Usage
GSCA(genedata,pattern,chipdata,scaledata=F,Pval.co=0.05,directory=NULL)
Arguments
genedata
A data.frame with three columns specifying the input genesets. Each row specifies an activated or repressed gene in a geneset. First column: character value
of geneset name specified by the user, could be any name easy to remember
e.g. GS1,GS2,...; Second column: numeric value of Entrez GeneID of the gene;
Third column: numeric value of single gene weight when calculating the activity level of the whole geneset. Positive values for activated gene and negative
values for repressed gene. Here, activated gene means that increases in expression of the gene also increases the overall activity of the whole geneset, while
increases in expression of the repressed genes will decrease the overall activity
of the whole geneset.
pattern
A data.frame with four columns indicating the activity patterns corresponding to
the given genedata. Each row specifies activity pattern for one geneset. First column: character value of the same geneset name used in genedata, each geneset
name in genedata should appear exactly once in this column. Second column:
GSCA
7
character value of whether high or low activity of the whole geneset is interested. "High" stands for high activity and "Low" stands for low activity. Third
column: character value of which cutoff type is going to be used. 3 cutoff types
can be specified: "Norm", "Quantile", or "Exprs". If cutoff type is "Norm", then
the fourth column should be specified as p-value between 0 and 1, where the
geneset expression cutoff will correspond to the specified p-value (one-sided)
based on a fitted normal distribution; If cutoff type is "Quantile", then the fourth
column should be specified as a desired quantile between 0 and 1, where the
geneset expression cutoff will correspond to the specified quantile. Finally, if
cutoff type is "Exprs", the geneset expression cutoff will be equal to the value
given in the fourth column. Fourth column: numeric value of cutoff value based
on different cutoff types specified in the third column.
chipdata
A character value of ’hgu133a’, ’hgu133A2’, ’hgu133Plus2’ or ’moe4302’.
This argument specifies which compendium to use. Requires the corresponding data package.
scaledata
logical value indicating whether expression data for each gene should be scaled
across samples to have mean 0 and variance 1.
Pval.co
A numeric value specifying the adjusted p-value cutoff. Only the biological
contexts with significant enrichment above the adjusted p-value cutoff will be
reported in the final ranked table output.
directory
Either null or a character value giving a directory path. If directory is not null,
then additional follow-up GSCA analyses will be performed and stored in the
folder specified by directory. If directory is null then no additional follow-up
GSCA analyses will be performed.
Details
GSCA requires as input user-specified genesets together with their corresponding activity patterns.
Each geneset contained the Entrez GeneID of activied and repressed genes. Activated gene means
that increases in expression of the gene also increases the overall activity of the whole geneset,
while repressed gene means that increases in expression of the gene decreases the overall activity
of the whole geneset.
GSCA also requires activity patterns of the genesets. Users can choose either high or low level of
activity for each geneset. Cutoffs are given by the users to determine what activity level should be
considered high or low. There are three types of cutoffs available: normal, quantile and expression
value. For normal cutoff type, a specified p-value (one-sided) based on a fitted normal distribution
will be used as cutoff, and all samples having p-value larger(smaller) than this p-value will be
considered having high(low) expression activity in a certain geneset.Likewise, for quantile cutoff
type, a quantile will be used as cutoff. As for cutoff type of expression level, a numeric value will
be directly used as cutoff.
GSCA then searches through the compendium for all samples that exhibit the specified activity
pattern of interest. For example, if activity patterns of all genesets are set to be high, then GSCA will
find all samples in the compendium that have greater geneset expression levels than the respective
cutoffs. Since each of the samples correspond to different biological contexts, the Fisher’s exact test
will then be used to test the association between each biological context and the geneset activity
pattern of interest based on the number of samples in each biological context that exhibits the
specified geneset activity pattern of interest.
8
GSCA
The final output is a ranked table of biological contexts enriched with the geneset activity pattern of
interest. The p-values are also adjusted by the Bonferroni correction.
If directory is not null, then GSCA will peform detail analyses for all contexts in each of the experimental IDs in the final GSCA results table. For each of the experiment IDs, tabSearch will be
run to locate all contexts in the compendium for that experiment ID, and then GSCAeda will be run
using the same genedata and pattern as input specific to the contexts recovered by tabSearch. See
GSCAeda for more details. Note, this automated process could be time-consuming and produce a
lot of files and directories.
Value
Returns a list with
Ranking
Data.frame of ranked table of biological contexts significantly enriched with the
specified geneset activity pattern. It includes information of Ranking, number
of samples exhibiting the given activity pattern, total number of samples, fold
change values, adjusted p-values, name of biological context and corresponding
experiment ID.
Score
Numeric matrix of geneset expression values for each sample in the compendium.
Each row stands for a certain geneset and each column stands for a certain sample.
Pattern
Data.frame of geneset activity pattern. The same as the input value.
Cutoff
Numeric vector of cutoff values calculated for each geneset based on the input
pattern.
SelectedSample Numeric vector of all samples that exhibits the given geneset activity pattern.
Totalgene
Numeric vector of total number of genes use to calculate the geneset activity in
each geneset
Missinggene
Numeric vector of number of genes that do not have corresponding expression
measuremnts on the platform
Species
Character value of the species analyzed.
If directory is not null, then pdf and csv files containing the GSCAeda follow-up analysis results
and plots in the directory folder will also be returned.
Author(s)
Zhicheng Ji, Hongkai Ji
References
George Wu, et al. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics
2013 Apr 23;29(9):1182-1189.
GSCAeda
9
Examples
## First load the TF target genes derived from Oct4 ChIPx data
## in embryonic stem cells. The data is in the form of a list
## where the first item contains the activated (+) target genes in
## Entrez GeneID format and the second item contains the repressed (-)
## target genes in Entrez GeneID format.
data(Oct4ESC_TG)
## We want to analyze Oct4, so we need to specify the EntrezGeneID for Oct4
## and input the activated (+) and repressed (-) target genes of Oct4.
## Constucting the input genedata required by GSCA. There are two genesets
## one is the TF and another is the TF target genes. Note that constructing genedata
## with many genesets could be laborious, so using the interactive UI is recommended to
## easily start up the analysis.
activenum <- length(Oct4ESC_TG[[1]])
repressnum <- length(Oct4ESC_TG[[2]])
Octgenedata <- data.frame(gsname=c("GS1",rep("GS2",activenum+repressnum)),gene=c(18999,Oct4ESC_TG[[1]],Oct4ESC_
## We are interested in the pattern that TF and its target genes are all highly expressed.
## We also need to define how high the cutoffs should be such
## that each cutoff corresponds to the p-value of 0.1
## based on fitted normal distributions.
## Constructing pattern required by GSCA, all geneset names in genedata should appear
## exactly once in the first column
Octpattern <- data.frame(gsname=c("GS1","GS2"),acttype="High",cotype="Norm",cutoff=0.1,stringsAsFactors=FALSE)
## Lastly, we specify the chipdata to be "moe4302" and the significance of enriched
## biological contexts must be at least 0.05 to be reported.
Octoutput <- GSCA(Octgenedata,Octpattern,"moe4302",Pval.co=0.05)
## The first item in the list 'Octoutput[[1]]' contains the ranked table, which
## can then be saved. Additionally, we may be interested in plotting the results
## to visualize the enriched biological contexts within given geneset activity.
## Here, N specifies the top 5 significant biological contexts.
## Since plotfile is NULL, the plot directly shows up in R.
## Check GSCAplot for more details.
GSCAplot(Octoutput,N=5,plotfile=NULL,Title="GSCA plot of Oct4 in ESC")
## If you would like detailed follow-up analyses to be automatically performed
## for the Oct4 analyses in ESCs, just specify a file directory.
## Check GSCAeda for more details.
Octoutput <- GSCA(Octgenedata,Octpattern,"moe4302",Pval.co=0.05,directory=tempdir())
## All output will be stored in the specified directory.
## This process may be time-consuming and generate a lot of files.
## Alternatively, see GSCAeda for more info on manual alternatives.
GSCAeda
GSCA follow-up exploratory data analysis
10
GSCAeda
Description
GSCAeda is used to further study GSCA significant predictions in more detail to obtain additional
insight into biological function. GSCAeda requires users to first run the tabSearch function to
identify the biological contexts of interest. By default, GSCAeda will run automatically after an
initial GSCA analysis by searching for all contexts related to the experimentID for each significant
GSCA prediction. Alternatively, users can use GSCAeda by itself to further study any geneset
or biological contexts of interest that are found in the compendium. The output of GSCAeda are
multiple plots displaying the geneset activity values and genes of interest in the input biological
contexts. Also included are the usual GSCA analysis results table showing the enrichment of each
contexts for the geneset activity pattern of interest, t-test results (t-statistics and p-values) for all
pair-wise combinations of inputted contexts in each geneset, and a summary of raw geneset activity
values for each context of interest. Users can then use the raw geneset activity values for further
statistical analyses if desired.
Usage
GSCAeda(genedata,pattern,chipdata,SearchOutput,scaledata=F,Pval.co=0.05,Ordering="Average",Title=NUL
Arguments
genedata
A data.frame with three columns specifying the input genesets. Each row specifies an activated or repressed gene in a geneset. First column: character value
of geneset name specified by the user, could be any name easy to remember
e.g. GS1,GS2,...; Second column: numeric value of Entrez GeneID of the gene;
Third column: numeric value of single gene weight when calculating the activity level of the whole geneset. Positive values for activated gene and negative
values for repressed gene. Here, activated gene means that increases in expression of the gene also increases the overall activity of the whole geneset, while
increases in expression of the repressed genes will decrease the overall activity
of the whole geneset.
pattern
A data.frame with four columns indicating the activity patterns corresponding to
the given genedata. Each row specifies activity pattern for one geneset. First column: character value of the same geneset name used in genedata, each geneset
name in genedata should appear exactly once in this column. Second column:
character value of whether high or low activity of the whole geneset is interested. "High" stands for high activity and "Low" stands for low activity. Third
column: character value of which cutoff type is going to be used. 3 cutoff types
can be specified: "Norm", "Quantile", or "Exprs". If cutoff type is "Norm", then
the fourth column should be specified as p-value between 0 and 1, where the
geneset expression cutoff will correspond to the specified p-value (one-sided)
based on a fitted normal distribution; If cutoff type is "Quantile", then the fourth
column should be specified as a desired quantile between 0 and 1, where the
geneset expression cutoff will correspond to the specified quantile. Finally, if
cutoff type is "Exprs", the geneset expression cutoff will be equal to the value
given in the fourth column. Fourth column: numeric value of cutoff value based
on different cutoff types specified in the third column.
chipdata
A character value of ’hgu133a’, ’hgu133A2’, ’hgu133Plus2’ or ’moe4302’.
GSCAeda
11
This argument specifies which compendium to use. Requires the corresponding data package.
scaledata
logical value indicating whether expression data for each gene should be scaled
across samples to have mean 0 and variance 1.
SearchOutput
Output of the tabSearch function. More specifically, a data frame where the 1st
column is the ExperimentIDs (GSE ids), the 2nd column is the SampleTypes,
and the 3rd column is the sample count for each SampleType.
Pval.co
A numeric value specifying the adjusted p-value cutoff. Only the biological
contexts with significant enrichment above the adjusted p-value cutoff will be
reported in the final ranked table output.
Ordering
A character value of either one geneset name or ’Average’. If Ordering is
one geneset name, the plot of geneset activity values and heatmap of the tstatistics/pvalues will be ordered from the highest to lowest according the Ordering geneset activity value. If Ordering is ’Average’, the plots and heatmap
will be organized by the average rank across all geneset activity values.
Title
Title of the plot, will appear on the top of the plot.
outputdir
Either null or a character value giving the directory in which GSCAeda will save
the output files.
Details
GSCAeda is designed to be used in combination with tabSearch after an initial GSCA analysis.
GSCAeda is used to further study each predicted biological context in more detail by comparing
the functional activity across related contexts through the geneset activities. To do so, GSCAeda requires users to specific genedata, pattern, species, pval cutoff, and the search results from tabSearch
containing the list of biological contexts of interest. Then GSCAeda will calculate the mean and
standard deviation of each geneset activity value for each inputted context, and will perform t-tests
comparing the mean geneset activity values for all pair-wise combinations of inputted contexts, and
test for enrichment of the geneset activity pattern of interest. The results will be shown in several
plots and tables(number of files varying with number of given genesets), along with the raw geneset
activity values for further followup statistical analyses. Check the value part of this help file to see
how GSCAeda saves the outputs. For information on the GSCA parameters, see the GSCA help file
which explains in more detail how functional enrichment of a geneset activity pattern of interest is
tested.
Value
If outputdir is specified, GSCAeda will first produce a boxplot depicting the distribution of all
geneset activities in different biological contexts of interest. Then, for each geneset GSCAeda will
produce tow heatmaps showing respectively the t-statistics and p-values obtained from the t-tests
testing the mean of geneset activity for each pair-wise combination of the input biological contexts.
Finally, GSCAeda will output two csv files. The first one contains the raw geneset activity values
for each input context and the second one contains the mean and standard deviation of the geneset
activity values for each context, the GSCA enrichment test results, and the p-values/t-statistics of
the t-tests. If outputdir is NULL, all plots and the result table will be directly displayed in the R
console.
12
GSCAplot
Author(s)
Zhicheng Ji, Hongkai Ji
References
George Wu, et al. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics
2013 Apr 23;29(9):1182-1189.
See Also
GSCA
Examples
library(GSCA)
## Load example STAT1 target genes defined ChIP-seq and literature
data(STAT1_TG)
## Construct genedata and pattern using the same way as GSCA
Statgenenum <- length(STAT1_TG)
Statgenedata <- data.frame(gsname=c("GS1",rep("GS2",Statgenenum)),gene=c(6772,STAT1_TG),weight=1,stringsAsFacto
Statpattern <- data.frame(gsname=c("GS1","GS2"),acttype="High",cotype="Norm",cutoff=0.1,stringsAsFactors=FALSE)
## Find all contexts in human compendium from GSE7123
GSE7123out <- tabSearch("GSE7123","hgu133a")
## Run GSCAeda
GSCAeda(Statgenedata,Statpattern,"hgu133a",GSE7123out,Pval.co=0.05,Ordering="Average",Title=NULL,outputdir=NULL
## To save the results, instead of displaying in R console, specifiy an outputdir argument
GSCAeda(Statgenedata,Statpattern,"hgu133a",GSE7123out,Pval.co=0.05,Ordering="Average",Title=NULL,outputdir=temp
GSCAplot
Visualize GSCA output
Description
GSCAplot visualizes the output from GSCA. For one geneset, GSCAplot makes histograms of
geneset activities for all samples and samples in each of most significantly enriched biological
contexts. For two genesets, GSCAplot makes a scatter plot of sample activities of first geneset
versus sample activities of second geneset plotting, and the most significantly enriched biological
contexts are highlighted in the plot. For more than two genesets, GSCAplot produces two heatmap
according to geneset activities. The first heatmap shows the geneset activities of all samples and
indicates which samples belong to enriched biological contexts. The second heatmap shows the
geneset activities of samples exhibiting given geneset activity pattern, and the most significantly
enriched biological contexts are highlighted.
GSCAplot
13
Usage
GSCAplot(GSCAoutput,N=5,plotfile=NULL,Title=NULL)
Arguments
GSCAoutput
Exact output from GSCA.
N
N is a numeric value ranging from 1 to 5. It specifies the number of top-ranked
biological contexts to plot from the GSCA analysis.
plotfile
A character value specifying the path to save the GSCA plot. If plotfile is null,
the plot will not be saved and will appear directly in R console.
Title
A character value specifying the title of the plot.
Details
GSCAplot is a plotting function that acts as an easy-to-use tool to visualize the GSCA output.
For one geneset, GSCAplot uses histogram() to first plot a histogram of geneset activities for all
samples in the compendium, then plot N histograms of geneset activities for samples in each of
top N most significantly enriched biological contexts. For two genesets, GSCAplots uses plot() to
make a scatterplot of all samples in the compendium where x-axis is the activity of the first geneset
and y-axis is the activity of the second geneset. Then it highlights the top N most significantly
enriched biological contexts in different colors and types. Cutoff of the two genesets will also
be represented on the scatterplot as one vertical and one horizontal dotted line. For more than
two genesets, GSCAplots uses heatmap.2() from gplots package to plot two heatmaps. In the first
heatmap, geneset activities of all samples in the compendium will be shown. A color legend will
be drawn on the left upper corner of the heatmap so that users will know the corresponding activity
value each color represents. Above the heatmap there is a color bar of light and dark blue indicating
which samples exhibit the specific geneset activity pattern. In the second heatmap, geneset activity
of all samples which exhibit the specific geneset activity pattern will be shown. A color bar above
the heatmap uses different colors to indicate top N most significantly enriched biological contexts.
A color legend will also appear in the left upper corner of the heatmap. If plotfile is not null,
then instead of showing the plots directly in the R console, GSCAplot will save the plots to the
designated filepath as a pdf file. Note that because there are a lot of samples in both human and
mouse compendiums, drawing the first heatmap (and sometimes the second heatmap) could take a
lot of time especially a large number of genesets are given. GSCAplot only supports a predefined
geneset activity pattern and basic plotting options. Users are encouraged to use the interactive UI
if they want to interactively determine the geneset activity pattern, gain more powerful plotting
options and further customize their plots.
Value
A plot consisting of several histograms, a scatterplot or two heatmaps will be returned, depending
on numbers of genesets users give.
Author(s)
Zhicheng Ji, Hongkai Ji
14
GSCAui
References
George Wu, et al. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics
2013 Apr 23;29(9):1182-1189.
Examples
## Constructing genedata and pattern.
## Example of mouse gene Gli1,Gli2 and Gli3, all members of GLI-Kruppel family. Their corresponding Entrez GeneID
gligenedata <- data.frame(gsname=c("Gli1","Gli2","Gli3"),gene=c(14632,14633,14634),weight=1,stringsAsFactors=FA
glipattern <- data.frame(gsname=c("Gli1","Gli2","Gli3"),acttype="High",cotype="Norm",cutoff=0.1,stringsAsFactor
## Case of one geneset: a set of histograms
## Note that for N too large sometimes there is figure margins too large error.
## Decrease N or try to enlarge the plotting area in R console.
oneout <- GSCA(gligenedata[1,],glipattern[1,],"moe4302")
GSCAplot(oneout,N=2)
## Case of two genesets: a scatterplot
twoout <- GSCA(gligenedata[-3,],glipattern[-3,],"moe4302")
GSCAplot(twoout)
## Case of three genesets: two heatmaps, press Enter to switch to the second heatmap
## May take some time, be patient
threeout <- GSCA(gligenedata,glipattern,"moe4302")
GSCAplot(threeout)
##
##
##
##
Same plots in designated file path, FILE, which is a pdf file.
If you want to further customize output plots, for example changing
range of x-axis, changing titles or altering display of enriched
biological contexts, please check out the interactive user interface.
GSCAplot(oneout,plotfile=tempfile("plot",fileext=".pdf"),N=2,Title="Demo of one geneset plot")
GSCAplot(twoout,plotfile=tempfile("plot",fileext=".pdf"),Title="Demo of two genesets plot")
GSCAplot(threeout,plotfile=tempfile("plot",fileext=".pdf"),Title="Demo of three genesets plot")
GSCAui
Launch GSCA interactive User Interface
Description
GSCAui initiates in the web browser an interactive user interface of GSCA built using R shiny. This
user interface enables users to easily perform nearly all standard GSCA functions in GSCA package, and provides more powerful and useful options to specify geneset activity patterns, investigate
interested biological contexts and customize output plots and tables. For a complete user manual of
GSCAui, please refer to the user manual included in the user interface.
Usage
GSCAui()
GSCAui
15
Details
The purpose of building GSCA interactive user interface is to provide an easy way for all users to
perform analysis tools offered by GSCA, even though the users do not have any prior knowledge
in computer programming or statistics. GSCAui provides users handy ways to input their original
dataset into the program. Users who do not have much experience using R may find themselves
having difficulties building genedata and pattern datasets required by standard GSCA functions. In
comparison, GSCAui offers more covenient ways to directly type in gene IDs and specify parameters like cutoff types using pull down menus. Users can also check instantly how many genes they
inputted are recorded in a given compendium and decide what geneset to be used in further analysis
process. GSCAui also provides users more flexible and direct means to specify geneset activity patterns. For different number of geneset, GSCAui will automatically generate control panels which
are most suitable for users to interactively choose the geneset activity patterns. Users can not only
specify geneset activity patterns using traditional GSCA options, but they can also choose geneset activity pattern on histograms, scatterplots and heatmaps by point and click, which makes the
process easier and more explicit. In addition, GSCAui offers more powerful analysis and plotting
options. Both p-value and foldchange cutoffs can be given interactively to select the enriched biological contexts. Besides displaying top ranked enriched biological contexts, users can also select
specific biological contexts to be displayed on the plot. Finally, users can specify plotting details
like x-axis range and titles of the plots if they want to keep the plots for future use. Thanks to the
shiny server, users can type in the URL: http://spark.rstudio.com/jzc19900805/GSCA/ to directly
launch the UI in their web browser. This does not require any dependent R packages or even R
itself installed on users computer. All required is a web browser and the URL. Please check the user
manual in the UI for more complete explanations.
Value
A user interface will be shown in users’ default web browser. R console will start listenting to a
random port.
Author(s)
Zhicheng Ji, Hongkai Ji
References
George Wu, et al. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics
2013 Apr 23;29(9):1182-1189.
See Also
GSCA
Examples
## Running this will launch the UI in users' default web browser.
## Not run:
GSCAui()
## End(Not run)
16
Oct4ESC_TG
Oct4ESC_TG
Oct4 activated (+) and repressed (-) target genes in embryonic stem
cells
Description
List of Oct4 target genes derived from ChIP-seq and gene expression data from embryonic stem
cells (ESCs). Activated target genes are the first item in the list and repressed target genes are the
second item in the list.
Usage
data(Oct4ESC_TG)
Format
The format is: List of 2 $ : chr [1:519] "100678" "106298" "14609" "12468" ... $ : chr [1:337]
"246703" "15441" "70579" "20333" ...
Details
Oct4 target genes are defined as genes that are both predicted to be TF-bound in E14 ESCs and
differentially expressed after Oct4 knockdown via RNAi in E14TG2a ESCs.
Source
Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core
transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17.
Loh YH, Wu Q, Chew JL, Vega VB et al. The Oct4 and Nanog transcription network regulates
pluripotency in mouse embryonic stem cells. Nat Genet 2006 Apr;38(4):431-40.
References
http://www.ncbi.nlm.nih.gov/geo/
Examples
data(Oct4ESC_TG)
STAT1_TG
STAT1_TG
17
STAT1 activated (+) target genes defined from experimental ChIP-seq
data and literature survey.
Description
List of STAT1 target genes derived from ChIP-seq data in Hela cells and further refined by making
sure each target gene was further supported by experiments in literature as described in GSE15353.
No represed target genes were defined.
Usage
data(STAT1_TG)
Format
The format is: chr [1:23] "9636" "2537" "2633" "1435" "103" "3433" "3434" ...
Details
STAT1 target genes are defined as TF-bound from Hela ChIP-seq data and then further verified as
target genes through literature survey. This procedure is described in GSE15353.
Source
Robertson G, Hirst M, Bainbridge M, Bilenky M et al. Genome-wide profiles of STAT1 DNA
association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods
2007 Aug;4(8):651-7.
References
http://www.ncbi.nlm.nih.gov/geo/
Examples
data(STAT1_TG)
18
tabSearch
tabSearch
Searches through GPL96, GPL1261, GPL570 or GPL571 compendium data for biological contexts of interest.
Description
tabSearch requires users to provide keyword(s), the species, and either ’AND’ or ’OR’. Then the
function uses grep and the keywords to iteratively search for biological contexts or experiment IDs
that match the keywords, where ’AND’ requires all recovered contexts to satisfiy all keywords and
’OR’ requires all recovered contexts to match at least one keyword.
Usage
tabSearch(keyword, chipdata, option = "OR")
Arguments
keyword
A character vector of biological context words or experiment IDs. e.g. ’liver’ or
’GSE7123’.
chipdata
A character value of ’hgu133a’, ’hgu133A2’, ’hgu133Plus2’ or ’moe4302’.
This argument specifies which compendium to use. Requires the corresponding data package.
option
Either ’AND’ or ’OR’ to specify whether the recovered contexts need to be
found by ALL keywords (AND) or found by at least one keyword (OR).
Details
If the users want to search for a specific list of contexts, simply input the contexts as a character
vector, where each element is a different context. Alternatively, the contexts can also be a series of
keywords in short-hand. The ’AND’ option is primarly used when users want to search for contexts
from a specific experiment. In most cases ’OR’ should be used.
After tabSearch finishes running, it will return a list of contexts that match the inputted keywords
and parameters. Users can then further study these contexts for activity of given gensets using the
function GSCAeda.
Value
A data frame consisting of three columns. The 1st column is the experiment ID, the 2nd column
is the biological context label, and the 3rd column is the number of samples for each biological
context.
Author(s)
Zhicheng Ji, Hongkai Ji
tabSearch
19
References
George Wu, et al. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics
2013 Apr 23;29(9):1182-1189.
Examples
library(GSCA)
## Search for all contexts in GSE7123 in hgu133a
tabSearch("GSE7123","hgu133a")
## Search for all contexts labeled 'fetal' or 'liver' in moe4302
tabSearch(c("Fetal","Liver"),"moe4302")
## Search for all contexts labeled 'fetal liver' AND in GSE13044 in moe4302
tabSearch(c("Fetal","GSE13044"),"moe4302","AND")
Index
∗Topic GSCAeda
GSCAeda, 9
∗Topic GSCAplot
GSCAplot, 12
∗Topic GSCAui
GSCAui, 14
∗Topic GSCA
GSCA, 6
∗Topic annotate
annotatePeaks, 3
∗Topic datasets
geneIDdata, 6
Oct4ESC_TG, 16
STAT1_TG, 17
∗Topic package, GSCA
GSCA-package, 2
∗Topic peaks
annotatePeaks, 3
∗Topic plot
GSCAplot, 12
∗Topic search
tabSearch, 18
∗Topic target genes
ConstructTG, 4
annotatePeaks, 3
ConstructTG, 4
geneIDdata, 6
GSCA, 6
GSCA-package, 2
GSCAeda, 9
GSCAplot, 12
GSCAui, 14
Oct4ESC_TG, 16
STAT1_TG, 17
tabSearch, 18
20