API - TFregulomeR

Quick links

1. Introduction
2. TFregulomeR data compendium and functionalities
3. TFregulomeR Installation
4. TFregulomeR Instructions
5. Cite

Introduction

TFregulomeR is an R-library linking to a compendium of transcription factor (TF) cistrome and methylome data, derived from MethMotif and GTRD databases, while containing essential functions in R programming language to facilitate data browsing, retrieval and analysis. In particular, TFregulomeR enables the query of context in/dependent cistrome, TF interactome (global view of TF interactions at the DNA binding levels) as well as cis-regulatory modules. All these facilitate i) context specific co-factor analysis coupled with DNA methylation, ii) motif deconvolution and iii) annotation of context-specific TF binding sites in terms of genomic locations and functions.

TFregulomeR data compendium and functionalities

1) TFregulomeR linked data compendium

item	Count
PWM	1,468
ChIP-seq experiments	3,891
Unique TF	415
PWM 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

2) TFregulomeR functionalities

1. Browse the TFregulomeR data warehouse (dataBrowser)
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)

TFregulomeR Installation

TFregulomeR source codes have been implemented in GitHub.

1) For stable release repository, please visit here.

2) For development release repository, please visit here.

3) For a local version of the TFregulomeR database, please download and unzip the file found here.

TFregulomeR Instructions

Please click here for TFregulomeR manual.

Please click here for TFregulomeR vignettes.

Cite

Currently, TFregulomeR manuscript has been accepted in Nucleic Acids Research.

If you are using TFregulomeR, please cite us as follows:

Quy Xiao Xuan Lin, Denis Thieffry, Sudhakar Jha, Touati Benoukraf. (2019) TFregulomeR reveals transcription factors’ context-specific features and functions. Nucleic Acids Res., 10.1093/nar/gkz1088. [Manuscript]