TY - JOUR

T1 - Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data

AU - Levitsky, Victor G.

AU - Mukhin, Alexey M.

AU - Oshchepkov, Dmitry Yu

AU - Zemlyanskaya, Elena V.

AU - Lashin, Sergey A.

N1 - Publisher Copyright: © 2022 by the authors.

PY - 2022/8/11

Y1 - 2022/8/11

N2 - (1) Background: The widespread application of ChIP-seq technology requires annotation of cis-regulatory modules through the search of co-occurred motifs. (2) Methods: We present the web server Motifs Co-Occurrence Tool (Web-MCOT) that for a single ChIP-seq dataset detects the composite elements (CEs) or overrepresented homo- and heterotypic pairs of motifs with spacers and overlaps, with any mutual orientations, uncovering various similarities to recognition models within pairs of motifs. The first (Anchor) motif in CEs respects the target transcription factor of the ChIP-seq experiment, while the second one (Partner) can be defined either by a user or a public library of Partner motifs being processed. (3) Results: Web-MCOT computes the significances of CEs without reference to motif conservation and those with more conserved Partner and Anchor motifs. Graphic results show histograms of CE abundance depending on orientations of motifs, overlap and spacer lengths; logos of the most common CE structural types with an overlap of motifs, and heatmaps depicting the abundance of CEs with one motif possessing higher conservation than another. (4) Conclusions: Novel capacities of Web-MCOT allow retrieving from a single ChIP-seq dataset with maximal information on the co-occurrence of motifs and potentiates planning of next ChIP-seq experiments.

AB - (1) Background: The widespread application of ChIP-seq technology requires annotation of cis-regulatory modules through the search of co-occurred motifs. (2) Methods: We present the web server Motifs Co-Occurrence Tool (Web-MCOT) that for a single ChIP-seq dataset detects the composite elements (CEs) or overrepresented homo- and heterotypic pairs of motifs with spacers and overlaps, with any mutual orientations, uncovering various similarities to recognition models within pairs of motifs. The first (Anchor) motif in CEs respects the target transcription factor of the ChIP-seq experiment, while the second one (Partner) can be defined either by a user or a public library of Partner motifs being processed. (3) Results: Web-MCOT computes the significances of CEs without reference to motif conservation and those with more conserved Partner and Anchor motifs. Graphic results show histograms of CE abundance depending on orientations of motifs, overlap and spacer lengths; logos of the most common CE structural types with an overlap of motifs, and heatmaps depicting the abundance of CEs with one motif possessing higher conservation than another. (4) Conclusions: Novel capacities of Web-MCOT allow retrieving from a single ChIP-seq dataset with maximal information on the co-occurrence of motifs and potentiates planning of next ChIP-seq experiments.

KW - chromatin immunoprecipitation with massively parallel sequencing

KW - co-binding of transcription factors

KW - composite elements

KW - motifs conservation

KW - overlap of motifs

KW - transcription factor binding sites

KW - transcription factors binding sites prediction

UR - http://www.scopus.com/inward/record.url?scp=85136642860&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/11845ab7-03d5-38ff-84e1-fcbff966e61a/

U2 - 10.3390/ijms23168981

DO - 10.3390/ijms23168981

M3 - Article

C2 - 36012247

AN - SCOPUS:85136642860

VL - 23

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 16

M1 - 8981

ER -