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      COCOA: coordinate covariation analysis of epigenetic heterogeneity

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          Abstract

          A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across individuals and a database of region sets to annotate epigenetic heterogeneity. COCOA is the first such tool for DNA methylation data and can also analyze any epigenetic signal with genomic coordinates. We demonstrate COCOA’s utility by analyzing DNA methylation, ATAC-seq, and multi-omic data in supervised and unsupervised analyses, showing that COCOA provides new understanding of inter-sample epigenetic variation. COCOA is available on Bioconductor ( http://bioconductor.org/packages/COCOA).

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

            The analysis of regulatory regions in genome sequences is strongly based on the detection of potential transcription factor binding sites. The preferred models for representation of transcription factor binding specificity have been termed position-specific scoring matrices. JASPAR is an open-access database of annotated, high-quality, matrix-based transcription factor binding site profiles for multicellular eukaryotes. The profiles were derived exclusively from sets of nucleotide sequences experimentally demonstrated to bind transcription factors. The database is complemented by a web interface for browsing, searching and subset selection, an online sequence analysis utility and a suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. JASPAR is available at http://jaspar. cgb.ki.se.
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              AP-1: a double-edged sword in tumorigenesis.

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                Author and article information

                Contributors
                nsheffield@virginia.edu
                Journal
                Genome Biol
                Genome Biol
                Genome Biology
                BioMed Central (London )
                1474-7596
                1474-760X
                7 September 2020
                7 September 2020
                2020
                : 21
                Affiliations
                [1 ]GRID grid.27755.32, ISNI 0000 0000 9136 933X, Department of Biomedical Engineering, , University of Virginia, ; Charlottesville, VA USA
                [2 ]GRID grid.27755.32, ISNI 0000 0000 9136 933X, Center for Public Health Genomics, , University of Virginia, ; Charlottesville, VA USA
                [3 ]GRID grid.27755.32, ISNI 0000 0000 9136 933X, Department of Biochemistry and Molecular Genetics, , University of Virginia, ; Charlottesville, VA USA
                [4 ]GRID grid.27755.32, ISNI 0000 0000 9136 933X, Department of Medicine, , University of Virginia, ; Charlottesville, VA USA
                [5 ]GRID grid.27755.32, ISNI 0000 0000 9136 933X, University of Virginia Cancer Center, ; Charlottesville, USA
                Article
                2139
                10.1186/s13059-020-02139-4
                7487606
                32894181
                20e7fe0a-5740-4915-8fa4-65f458e40a1e
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                Funding
                Funded by: National Institute of General Medical Sciences (US)
                Award ID: GM128636
                Award Recipient :
                Categories
                Method
                Custom metadata
                © The Author(s) 2020

                Genetics
                epigenetics,dna methylation,chromatin accessibility,principal component analysis,dimensionality reduction,data integration,cancer,ezh2,multi-omics

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