Open Access

TFBSPred: A functional transcription factor binding site prediction webtool for humans and mice

  • Authors:
    • Vasileios L. Zogopoulos
    • Katerina Spaho
    • Chaido Ntouka
    • Gerasimos A. Lappas
    • Ioannis Kyranis
    • Pantelis G. Bagos
    • Demetrios A. Spandidos
    • Ioannis Michalopoulos
  • View Affiliations

  • Published online on: September 3, 2021     https://doi.org/10.3892/ije.2021.9
  • Article Number: 9
  • Copyright: © Zogopoulos et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Transcription factors (TFs) play a major role in the regulation of gene expression. Discovering the TFs which bind to the regulatory regions of each gene has been long‑term focus of research. Since the experimental verification of TF binding sites (TFBSs) is a complex process, webtools that perform predictions have been developed. However, the majority of the tools do not provide a user‑friendly environment for data input and a number of these tools produce a large number of false‑positive results. The present study introduces TFBSPred, a TFBS prediction webtool that utilises hidden Markov model‑based TF flexible models (TFFM) for predicting binding sites while providing an automated and minimal input user interface. TFBSPred uses DNAse I hypersensitivity data from ENCODE to identify open chromatin regions and takes advantage of the conservation between Homo sapiens and Mus musculus, by using Ensembl Compara pairwise alignments, to increase the true positive rate of the prediction. The users input a gene name or genomic location of a human or mouse genome, select the cell types of interest and TFBSPred outputs the conserved open chromatin region of the selected regulatory sequences and cell types as a pairwise alignment and displays the predicted TFBSs. The present study benchmarked TFBSPred and several similar functioning webtools using experimentally verified TFBSs. TFBSPred exhibited the optimal trade‑off between sensitivity and specificity in the case of the well‑studied IFNB1 enhanceosome, while outperforming the other web tools in subsequent use‑cases. TFBSPred may thus prove to be a valuable tool for TFBS prediction and for the provision of hypotheses for experimental validation. TFBSPred also has the potential for further improvement with future updates of TFFM data. TFBSPred is freely available at: https://www.michalopoulos.net/tfbspred/.

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November-December 2021
Volume 1 Issue 4

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Copy and paste a formatted citation
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Spandidos Publications style
Zogopoulos VL, Spaho K, Ntouka C, Lappas GA, Kyranis I, Bagos PG, Spandidos DA and Michalopoulos I: TFBSPred: A functional transcription factor binding site prediction webtool for humans and mice. Int J Epigen 1: 9, 2021
APA
Zogopoulos, V.L., Spaho, K., Ntouka, C., Lappas, G.A., Kyranis, I., Bagos, P.G. ... Michalopoulos, I. (2021). TFBSPred: A functional transcription factor binding site prediction webtool for humans and mice. International Journal of Epigenetics, 1, 9. https://doi.org/10.3892/ije.2021.9
MLA
Zogopoulos, V. L., Spaho, K., Ntouka, C., Lappas, G. A., Kyranis, I., Bagos, P. G., Spandidos, D. A., Michalopoulos, I."TFBSPred: A functional transcription factor binding site prediction webtool for humans and mice". International Journal of Epigenetics 1.4 (2021): 9.
Chicago
Zogopoulos, V. L., Spaho, K., Ntouka, C., Lappas, G. A., Kyranis, I., Bagos, P. G., Spandidos, D. A., Michalopoulos, I."TFBSPred: A functional transcription factor binding site prediction webtool for humans and mice". International Journal of Epigenetics 1, no. 4 (2021): 9. https://doi.org/10.3892/ije.2021.9