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CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana. / Lavrekha, Viktoriya V.; Levitsky, Victor G.; Tsukanov, Anton V. et al.

In: Frontiers in Plant Science, Vol. 13, 942710, 18.08.2022.

Research output: Contribution to journalArticlepeer-review

Harvard

APA

Lavrekha, V. V., Levitsky, V. G., Tsukanov, A. V., Bogomolov, A. G., Grigorovich, D. A., Omelyanchuk, N., Ubogoeva, E. V., Zemlyanskaya, E. V., & Mironova, V. (2022). CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana. Frontiers in Plant Science, 13, [942710]. https://doi.org/10.3389/fpls.2022.942710

Vancouver

Lavrekha VV, Levitsky VG, Tsukanov AV, Bogomolov AG, Grigorovich DA, Omelyanchuk N et al. CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana. Frontiers in Plant Science. 2022 Aug 18;13:942710. doi: 10.3389/fpls.2022.942710

Author

Lavrekha, Viktoriya V. ; Levitsky, Victor G. ; Tsukanov, Anton V. et al. / CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana. In: Frontiers in Plant Science. 2022 ; Vol. 13.

BibTeX

@article{fbb412b8743a4d94837c7727e315d3d7,
title = "CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana",
abstract = "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.",
keywords = "DAP-seq, multi-omics data integration, proximal promoters, RNA-seq, transcription factor binding profiles",
author = "Lavrekha, {Viktoriya V.} and Levitsky, {Victor G.} and Tsukanov, {Anton V.} and Bogomolov, {Anton G.} and Grigorovich, {Dmitry A.} and Nadya Omelyanchuk and Ubogoeva, {Elena V.} and Zemlyanskaya, {Elena V.} and Victoria Mironova",
note = "Funding Information: Re-processing of DAP-seq datasets was done in the frame of the project supported by Russian Science Foundation 21-14-00240. CisCross web service development was supported by Russian Foundation for Basic Research RFBR-DFG-19-54-12013. Processing of raw data was performed using computational resources of the “Bioinformatics” Joint Computational Center supported by the State Budget Project FWNR-2022-0020. VM was supported by RIBES, Radboud University. Publisher Copyright: Copyright {\textcopyright} 2022 Lavrekha, Levitsky, Tsukanov, Bogomolov, Grigorovich, Omelyanchuk, Ubogoeva, Zemlyanskaya and Mironova.",
year = "2022",
month = aug,
day = "18",
doi = "10.3389/fpls.2022.942710",
language = "English",
volume = "13",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media S.A.",

}

RIS

TY - JOUR

T1 - CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana

AU - Lavrekha, Viktoriya V.

AU - Levitsky, Victor G.

AU - Tsukanov, Anton V.

AU - Bogomolov, Anton G.

AU - Grigorovich, Dmitry A.

AU - Omelyanchuk, Nadya

AU - Ubogoeva, Elena V.

AU - Zemlyanskaya, Elena V.

AU - Mironova, Victoria

N1 - Funding Information: Re-processing of DAP-seq datasets was done in the frame of the project supported by Russian Science Foundation 21-14-00240. CisCross web service development was supported by Russian Foundation for Basic Research RFBR-DFG-19-54-12013. Processing of raw data was performed using computational resources of the “Bioinformatics” Joint Computational Center supported by the State Budget Project FWNR-2022-0020. VM was supported by RIBES, Radboud University. Publisher Copyright: Copyright © 2022 Lavrekha, Levitsky, Tsukanov, Bogomolov, Grigorovich, Omelyanchuk, Ubogoeva, Zemlyanskaya and Mironova.

PY - 2022/8/18

Y1 - 2022/8/18

N2 - 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.

AB - 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.

KW - DAP-seq

KW - multi-omics data integration

KW - proximal promoters

KW - RNA-seq

KW - transcription factor binding profiles

UR - http://www.scopus.com/inward/record.url?scp=85137662428&partnerID=8YFLogxK

U2 - 10.3389/fpls.2022.942710

DO - 10.3389/fpls.2022.942710

M3 - Article

C2 - 36061801

AN - SCOPUS:85137662428

VL - 13

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 942710

ER -

ID: 38051089