TFregulomeR

Version: 1.1.0

Introduction

TFregulomeR comprises of a comprehensive compendium of transcription factor binding sites (TFBSs) derived from the MethMotif and GTRD, as well as the ready-to-use functionality in R language facilitating data access, integration and analysis. The binding motifs predicted in-silico from MethMotif and GTRD describe cell specific transcription factor (TF) binding propensities, while the DNA methylation profiles from MethMotif portray a second epigenetic dimension in TF binding events. The whole toolbox allows a better understanding of the TF binding propensities in a cell-specific manner.

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Release notes

This repository is TFregulomeR stable release

Current TFregulomeR development version: 1.1.0 (Updated on 25 July 2019).

For development release, please visit TFregulomeR-dev

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Documentation

You can check detailed package instructions in Vignettes

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Current Functionalities v1.1.0

Click here for functionality update notes

1. Browse the TFregulomeR data warehouse (TFBSBrowser)
2. Load TF peaks (loadPeaks)
3. Search motif matrix and DNA methylation score matrix (searchMotif)
4. Plot motif or MethMotif logo (plotLogo)
5. Export motif matrix and DNA methylation score matrix (exportMMPFM)
6. Get context-independent peaks along with DNA methylation profiles (commonPeaks & commonPeakResult)
7. Get context-dependent peaks along with DNA methylation profiles (exclusivePeaks & exclusivePeakResult)
8. Form a intersected matrix between two lists of peak sets along with DNA methylation profiles and read enrichments, for interactome and co-binding partner studies (intersectPeakMatrix & intersectPeakMatrixResult)
9. Automatically generate a PDF report for TF co-factors along with motif sequences, DNA methylation (within motif and in 200bp regions) and read enrichments (cofactorReport).
10. Plot the TFBS distribution in a given list of peak sets (motifDistrib & plotDistrib)
11. Annotate peak genomic locations (genomeAnnotate)
12. Annotate ontologies of target genes by a peak set (greatAnnotate)
13. Convert a motif matrix to a PFMatrix calss object for TFBSTools package (toTFBSTools)

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Current TFBSs in TFregulomeR compendium

Click here for TFregulomeR compendium update notes

TFregulomeR data compendium version: 1.1.0

Item	Count
TFBS	1468
ChIP-seq experiments	3891
Unique TF	415
TFBS with DNA methylation records	655
Species	human (hg38)
Organ	stem_cell, blood_and_lymph, connective_tissue, colorectum, brain, bone, stomach, prostate, breast, pancreas, skin, kidney, lung, eye, esophagus, heart, muscle, uterus, spleen, cervix, testis, liver, adrenal_gland, neck_and_mouth, pleura, ovary, thymus, fallopian, vagina
Sample type	primary_cells, cell_line, tissue
Cell or tissue	414
Disease state	normal, tumor, Simpson_Golabi_Behmel_syndrome, progeria, metaplasia, unknown, immortalized, premetastatic
Source	GTRD, MethMotif

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Citation

A manuscript describing TFregulomeR has been submitted for peer review. If you currently use TFregulomeR, please cite us as follows:

Quy Xiao Xuan Lin, Denis Thieffry, Sudhakar Jha, Touati Benoukraf. TFregulomeR reveals transcription factors’ context-specific features and functions. 2019. https://github.com/benoukraflab/TFregulomeR

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Case studies

The scripts of case studies used in our manuscript are available as below.

1. Case study of CEBPB
2. Case study of MAFF
3. Case study of ATF3

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Installation

Prerequisite packages (Will be installed automatically)

1. Required packages: the packages below are the basic prerequisite packages for TFregulomeR functionalities

   • jsonlite (>= 1.5)
   • ggplot2 (>= 3.0.0)
   • ggseqlogo (>= 0.1)
   • gridExtra (>= 2.3)
   • GenomicRanges (>= 1.32.7)
   • curl (>= 3.2)

2. Optional packages: the packages below are optional since they are required only in some functions or some options in a function

   • rGREAT (>= 1.14.0): only requried in greatAnnotate()
   • liftOver (>= 1.4.0): only required when users use hg38 peaks in greatAnnotate(). Since GREAT analysis doesn't support hg38, hg38 peaks will be converted to hg19 using liftOver.
   • rbokeh (>= 0.5.0): only required when users opt to export an intuitive HTML report in greatAnnotate()
   • TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.0): only required when users opt to annotate hg38 peak locations in genomeAnnotate()
   • TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2): only required when users opt to annotate hg19 peak locations in genomeAnnotate()
   • TFBSTools (>= 1.20.0): only required in toTFBSTools()

Install

In R console,

# if you have not installed "devtools" package
install.packages("devtools")
devtools::install_github("benoukraflab/TFregulomeR")

The step above will automatically install the required packages. However, you still need to install optional packages if you opt to use the functions such as greatAnnotate(), genomeAnnotate() and toTFBSTools().

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License

Artistic-2.0