| Type: | Package |
| Title: | Enrichment Approach to Predict Which Transcription Factors are Regulated |
| Version: | 0.99.0 |
| Description: | R implementation of 'TFactS' to predict which are the transcription factors (TFs), regulated in a biological condition based on lists of differentially expressed genes (DEGs) obtained from transcriptome experiments. This package is based on the 'TFactS' concept by Essaghir et al. (2010) <doi:10.1093/nar/gkq149> and expands it. It allows users to perform 'TFactS'-like enrichment approach. The package can import and use the original catalogue file from the 'TFactS' as well as users' defined catalogues of interest that are not supported by 'TFactS' (e.g., Arabidopsis). |
| License: | GPL-3 |
| URL: | https://afukushima.github.io/TFactSR/ |
| Depends: | R (≥ 4.3.0) |
| Imports: | qvalue, stats |
| Suggests: | BiocStyle, knitr, rmarkdown, spelling, testthat |
| VignetteBuilder: | knitr |
| biocViews: | Network, Software, DifferentialExpression, GeneTarget, GeneExpression, Microarray, RNASeq, Transcription, NetworkEnrichment |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Language: | en-US |
| NeedsCompilation: | no |
| Packaged: | 2023-08-31 00:35:51 UTC; fuku |
| Author: | Atsushi Fukushima 
[aut, cre] |
| Maintainer: | Atsushi Fukushima <afukushima@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2023-08-31 14:00:08 UTC |
A list of TF-target genes (TG) in Arabidopsis thaliana.
Description
A catalogue of annotated target genes in Arabidopsis thaliana
Details
The original regulatory network datasets were downloaded from AtRegNet - AGRIS Arabidopsis (http://arabidopsis.med.ohio-state.edu/moreNetwork.html) and ATRM (http://atrm.cbi.pku.edu.cn/), respectively. Then we integrated them based on AGI code.
The catalogues version is 0.0.1.
Value
None
Author(s)
Atsushi Fukushima
References
Yilmaz A et al. NAR 39:D1118-1122 (2011)
An example list of DEGs from DEMO data in TFactS.
Description
An example list of differentially expressed genes (DEGs).
Details
This was from DEMO data in TFactS (http://www.tfacts.org/). The list corresponds to 18 up-regulated genes.
Value
None
Author(s)
Atsushi Fukushima
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
An example list of 39 DEGs from DEMO data in TFactS.
Description
A list of 39 differentially expressed genes (DEGs).
Details
This was from DEMO data in TFactS (http://www.tfacts.org/). The list corresponds to 18 up-regulated genes and 21 down-regulated genes.
Value
None
Author(s)
Atsushi Fukushima
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
calculates Random Control (RC) fastly?
Description
This function calculates Random Control (RC)
Usage
FASTcalculateRC(
df,
DEGs,
catalog,
TFs,
all.targets,
TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME.",
lambda = 0.05,
nRep = 100
)
Arguments
df |
a data frame containng p-values |
DEGs |
a character vector of DEGs (differentially expressed genes) |
catalog |
a data frame of TFactS catalog (ver. 2) |
TFs |
a character vector of transcription factor |
all.targets |
a character vector of all target genes |
TF.col |
the name of the column that contains the TF names |
lambda |
a user-specified threshold of E-value (default: 0.05) |
nRep |
number of random selections (default: 100) |
Value
data.frame
Author(s)
Atsushi Fukushima
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
Examples
data(example.df)
data(catalog)
data(DEGs)
tftg <- extractTFTG(DEGs, catalog)
TFs <- tftg$TFs
all.targets <- tftg$all.targets
res <- FASTcalculateRC(example.df, DEGs, catalog, TFs, all.targets)
An example list of 74 DEGs from AtGenExpress stress dataset.
Description
A list of 74 differentially expressed genes (DEGs) from AtGenExpress
Details
This was from DEMO data in the Supplemental data (Table S4. Genes regulated by UV-B light stress in roots and shoots; filename: TPJ_3052_sm_TabS4.xls) of the paper by Killian et al. TPJ (2008). The list corresponds to 74 genes up-regulated in roots and shoots 1 hour after onset of UV-B stress treatment.
Value
None
Author(s)
Atsushi Fukushima
References
Killian J et al. Plant J. 2007 Apr;50(2):347-363.
TFactSR: A package for identifying critical transcription factors.
Description
TFactS is to predict which are the transcription factors (TFs), regulated in a biological condition based on lists of differentially expressed genes (DEGs) obtained from transcriptome experiments. This package is based on the TFactS concept and expands it. It allows users to performe TFactS-like enrichment approach. The package can import and use the original catalogue file from the TFactS website (http://www.tfacts.org/) as well as users' defined catalogues of interest that are not supported by TFactS (e.g., Arabidopsis).
performs enrichment analysis
Description
This function performs enrichment test (ET) based on Fisher's exact test
Usage
calculateEnrichmentTest(
DEGs,
catalog,
TFs,
TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME."
)
Arguments
DEGs |
a character vector of DEGs (differentially expressed genes) |
catalog |
a data frame of TFactS catalog (ver. 2) |
TFs |
a character vector of transcription factor |
TF.col |
the name of the column that contains the TF names |
Value
data.frame
Author(s)
Atsushi Fukushima Definition: m is the number of target genes annotated for the TF under consideration n is the number of query genes N is the number of regulations in the catalog k is the number of query genes that are annotated as regulated by TF (i.e., the intersection between the query and the TF signature)
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
Examples
data(DEGs)
data(catalog)
tftg <- extractTFTG(DEGs, catalog)
TFs <- tftg$TFs
res <- calculateEnrichmentTest(DEGs, catalog, TFs)
calculates E-value
Description
This function calculates E-value based on .
Usage
calculateEvalue(df, TFs)
Arguments
df |
a data frame containng p-values |
TFs |
a character vector of transcription factor |
Value
data.frame
Author(s)
Atsushi Fukushima
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
Examples
data(DEGs)
data(catalog)
tftg <- extractTFTG(DEGs, catalog)
TFs <- tftg$TFs
p.value <- runif(10)/(1:10)
df <- data.frame(p.value = p.value)
res <- calculateEvalue(df, TFs)
calculates FDR by Benjamini and Hochberg method
Description
This function calculates FDR based on BH.
Usage
calculateFDRBH(df)
Arguments
df |
a data frame containng p-values |
Value
data.frame
Author(s)
Atsushi Fukushima
References
Benjamini Y and Hochberg Y, J Roy Stat Soc B 57: 289?300 (1995)
Examples
p.value <- runif(10)/(1:10)
df <- data.frame(p.value = p.value)
res <- calculateFDRBH(df)
calculates Q-value
Description
This function calculates Q-value based on Storey.
Usage
calculateQvalue(df, lambda = seq(0.05, 0.5, 0.01))
Arguments
df |
a data frame containng p-values |
lambda |
a vector of the lambda values utilized to obtain pi0.lambda |
Value
data.frame
Author(s)
Atsushi Fukushima
References
Storey JD, The Annals of Statistics 31:2013-2035 (2003)
Examples
data(example.df)
p.value <- example.df$p.value
df <- data.frame(p.value = p.value)
res <- calculateQvalue(df)
calculates Random Control (RC)
Description
This function calculates Random Control (RC)
Usage
calculateRC(
df,
DEGs,
catalog,
TFs,
all.targets,
TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME.",
lambda = 0.05,
nRep = 100
)
Arguments
df |
a data frame containng p-values |
DEGs |
a character vector of DEGs (differentially expressed genes) |
catalog |
a data frame of TFactS catalog (ver. 2) |
TFs |
a character vector of transcription factor |
all.targets |
a character vector of all target genes |
TF.col |
the name of the column that contains the TF names |
lambda |
a user-specified threshold of E-value (default: 0.05) |
nRep |
number of random selections (default: 100) |
Value
data.frame
Author(s)
Atsushi Fukushima Definition: m is the number of target genes annotated for the TF under consideration n is the number of query genes N is the number of regulations in the catalog k is the number of query genes that are annotated as regulated by TF (i.e., the intersection between the query and the TF signature)
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
Examples
data(example.df)
data(catalog)
data(DEGs)
tftg <- extractTFTG(DEGs, catalog)
TFs <- tftg$TFs
all.targets <- tftg$all.targets
res <- calculateRC(example.df, DEGs, catalog, TFs, all.targets)
calculates TFactS
Description
This function calculates TFactS
Usage
calculateTFactS(
DEGs,
catalog,
TFs,
all.targets,
Q.value = FALSE,
lambda1 = seq(0.05, 0.5, 0.01),
lambda2 = 0.05,
nRep = 100,
TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME."
)
Arguments
DEGs |
a character vector of DEGs (differentially expressed genes) |
catalog |
a data frame of TFactS catalog (ver. 2) |
TFs |
a character vector of transcription factor |
all.targets |
a character vector of all target genes |
Q.value |
logical. If it is TRUE, Q.value by Storey method. |
lambda1 |
a vector of the lambda values utilized to obtain pi0.lambda |
lambda2 |
a user-specified threshold of E-value (default: 0.05) |
nRep |
number of random selections (default: 100) |
TF.col |
the name of the column that contains the TF names |
Value
data.frame
Author(s)
Atsushi Fukushima
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
Examples
data(DEGs)
data(catalog)
tftg <- extractTFTG(DEGs, catalog)
TFs <- tftg$TFs
all.targets <- tftg$all.targets
res <- calculateTFactS(DEGs, catalog, TFs, all.targets)
A list of TF-target genes (TG) in TFactS.
Description
A catalogue of annotated target genes based on TFactS.
Details
This was downloaded from TFactS (http://www.tfacts.org/).
The catalogues version is 2 (http://www.tfacts.org/TFactS-new/TFactS-v2/tfacts/data/Catalogues.xls).
Value
None
Author(s)
Atsushi Fukushima
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
An example result of enrichment analysis
Description
An example result of enrichment analysis
Details
The size of data frame is 345 TFs and 6 columns.
Value
None
Author(s)
Atsushi Fukushima
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
An example list of result of enrichment analysis
Description
An example list of result of enrichment analysis
Details
The length of the list is 345 (TFs).
Value
None
Author(s)
Atsushi Fukushima
References
Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.
extracts transcription factor (TF) and target gene (TG) information
Description
This function extracts information about transcription factor (TF) and target gene (TG) with TFactS Catalogue (v2).
Usage
extractTFTG(
DEGs,
catalog,
TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME.",
TG.col = "Target.gene..OFFICIAL_GENE_NAME."
)
Arguments
DEGs |
a character vector of DEGs (differentially expressed genes) |
catalog |
a data frame of TFactS catalog (ver. 2) |
TF.col |
the name of the column that contains the TF names |
TG.col |
the name of the column that contains the TG names |
Value
list
Author(s)
Atsushi Fukushima
Examples
data(DEGs)
data(catalog)
res <- extractTFTG(DEGs, catalog)
head(res$TFs)
formats the result of enrichment test (ET)
Description
This function formats the result of enrichment test (ET) based on Fisher's exact test
Usage
formatET(list)
Arguments
list |
a list of the result of enrichment test (ncol = 6) |
Value
data.frame
Author(s)
Atsushi Fukushima
Examples
data(example.list)
res <- formatET(example.list)
formats the result of Random Control (RC)
Description
This function formats the result of Random Control (RC) with random simulation based on Fisher's exact test
Usage
formatRC(df, list, nRep)
Arguments
df |
a data frame of ET including E-values, FDR-BH, and Q-values |
list |
a list of the result of RC (ncol = 2) |
nRep |
the number of random selections (negative control) |
Value
data.frame
Author(s)
Atsushi Fukushima
Examples
data(example.df)
data(example.list)
nRep <- 100
res <- formatRC(example.df, example.list, nRep)