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CREPE: a Shiny app for transcription factor cataloguing

SUMMARY: Transcription factors (TFs) are proteins that directly interpret the genome to regulate gene expression and determine cellular phenotypes. TF identification is a common first step in unraveling gene regulatory networks. We present CREPE, an R Shiny app to catalogue and annotate TFs. CREPE w...

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Detalles Bibliográficos
Autores principales: Rosado-Tristani, Diego A, Rodríguez-Martínez, José A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10162806/
https://www.ncbi.nlm.nih.gov/pubmed/37153629
http://dx.doi.org/10.1093/bioadv/vbad055
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author Rosado-Tristani, Diego A
Rodríguez-Martínez, José A
author_facet Rosado-Tristani, Diego A
Rodríguez-Martínez, José A
author_sort Rosado-Tristani, Diego A
collection PubMed
description SUMMARY: Transcription factors (TFs) are proteins that directly interpret the genome to regulate gene expression and determine cellular phenotypes. TF identification is a common first step in unraveling gene regulatory networks. We present CREPE, an R Shiny app to catalogue and annotate TFs. CREPE was benchmarked against curated human TF datasets. Next, we use CREPE to explore the TF repertoires of Heliconius erato and Heliconius melpomene butterflies. AVAILABILITY AND IMPLEMENTATION: CREPE is available as a Shiny app package available at GitHub (github.com/dirostri/CREPE). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.
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spelling pubmed-101628062023-05-06 CREPE: a Shiny app for transcription factor cataloguing Rosado-Tristani, Diego A Rodríguez-Martínez, José A Bioinform Adv Application Note SUMMARY: Transcription factors (TFs) are proteins that directly interpret the genome to regulate gene expression and determine cellular phenotypes. TF identification is a common first step in unraveling gene regulatory networks. We present CREPE, an R Shiny app to catalogue and annotate TFs. CREPE was benchmarked against curated human TF datasets. Next, we use CREPE to explore the TF repertoires of Heliconius erato and Heliconius melpomene butterflies. AVAILABILITY AND IMPLEMENTATION: CREPE is available as a Shiny app package available at GitHub (github.com/dirostri/CREPE). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online. Oxford University Press 2023-04-21 /pmc/articles/PMC10162806/ /pubmed/37153629 http://dx.doi.org/10.1093/bioadv/vbad055 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Application Note
Rosado-Tristani, Diego A
Rodríguez-Martínez, José A
CREPE: a Shiny app for transcription factor cataloguing
title CREPE: a Shiny app for transcription factor cataloguing
title_full CREPE: a Shiny app for transcription factor cataloguing
title_fullStr CREPE: a Shiny app for transcription factor cataloguing
title_full_unstemmed CREPE: a Shiny app for transcription factor cataloguing
title_short CREPE: a Shiny app for transcription factor cataloguing
title_sort crepe: a shiny app for transcription factor cataloguing
topic Application Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10162806/
https://www.ncbi.nlm.nih.gov/pubmed/37153629
http://dx.doi.org/10.1093/bioadv/vbad055
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