Research output: Contribution to journal › Article › peer-review
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 journal › Article › peer-review
}
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