TFmotifView

http://bardet.u-strasbg.fr/tfmotifview/?results=example

Methods

linear single view single scale single focus contiguous no abstraction linear parallel arrangement no interconnection point contiguous type segment contiguous type

Tool

Access Format web application
Supported Files bed
License Creative Commons Attribution License
Tool name

TFmotifView
Tool Link http://bardet.u-strasbg.fr/tfmotifview/
Documentation http://bardet.u-strasbg.fr/tfmotifview/

Paper

TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions

Clémentine Leporcq, Yannick Spill, Delphine Balaramane, Christophe Toussaint, Michaël Weber, Anaïs Flore Bardet, TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W208–W217, https://doi.org/10.1093/nar/gkaa252

Abstract

Transcription factors (TFs) regulate the expression of gene expression. The binding specificities of many TFs have been deciphered and summarized as position-weight matrices, also called TF motifs. Despite the availability of hundreds of known TF motifs in databases, it remains non-trivial to quickly query and visualize the enrichment of known TF motifs in genomic regions of interest. Towards this goal, we developed TFmotifView, a web server that allows to study the distribution of known TF motifs in genomic regions. Based on input genomic regions and selected TF motifs, TFmotifView performs an overlap of the genomic regions with TF motif occurrences identified using a dynamic P-value threshold. TFmotifView generates three different outputs: (i) an enrichment table and scatterplot calculating the significance of TF motif occurrences in genomic regions compared to control regions, (ii) a genomic view of the organisation of TF motifs in each genomic region and (iii) a metaplot summarizing the position of TF motifs relative to the center of the regions. TFmotifView will contribute to the integration of TF motif information with a wide range of genomic datasets towards the goal to better understand the regulation of gene expression by transcription factors. TFmotifView is freely available at http://bardet.u-strasbg.fr/tfmotifview/.