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CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana
Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, m...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434332/ https://www.ncbi.nlm.nih.gov/pubmed/36061801 http://dx.doi.org/10.3389/fpls.2022.942710 |
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author | Lavrekha, Viktoriya V. Levitsky, Victor G. Tsukanov, Anton V. Bogomolov, Anton G. Grigorovich, Dmitry A. Omelyanchuk, Nadya Ubogoeva, Elena V. Zemlyanskaya, Elena V. Mironova, Victoria |
author_facet | Lavrekha, Viktoriya V. Levitsky, Victor G. Tsukanov, Anton V. Bogomolov, Anton G. Grigorovich, Dmitry A. Omelyanchuk, Nadya Ubogoeva, Elena V. Zemlyanskaya, Elena V. Mironova, Victoria |
author_sort | Lavrekha, Viktoriya V. |
collection | PubMed |
description | Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana genes. |
format | Online Article Text |
id | pubmed-9434332 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-94343322022-09-02 CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana Lavrekha, Viktoriya V. Levitsky, Victor G. Tsukanov, Anton V. Bogomolov, Anton G. Grigorovich, Dmitry A. Omelyanchuk, Nadya Ubogoeva, Elena V. Zemlyanskaya, Elena V. Mironova, Victoria Front Plant Sci Plant Science Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana genes. Frontiers Media S.A. 2022-08-18 /pmc/articles/PMC9434332/ /pubmed/36061801 http://dx.doi.org/10.3389/fpls.2022.942710 Text en Copyright © 2022 Lavrekha, Levitsky, Tsukanov, Bogomolov, Grigorovich, Omelyanchuk, Ubogoeva, Zemlyanskaya and Mironova. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Lavrekha, Viktoriya V. Levitsky, Victor G. Tsukanov, Anton V. Bogomolov, Anton G. Grigorovich, Dmitry A. Omelyanchuk, Nadya Ubogoeva, Elena V. Zemlyanskaya, Elena V. Mironova, Victoria CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana |
title | CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana |
title_full | CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana |
title_fullStr | CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana |
title_full_unstemmed | CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana |
title_short | CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana |
title_sort | ciscross: a gene list enrichment analysis to predict upstream regulators in arabidopsis thaliana |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434332/ https://www.ncbi.nlm.nih.gov/pubmed/36061801 http://dx.doi.org/10.3389/fpls.2022.942710 |
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