title: Multiscale representation of genomic signals.
abstract: Genomic information is encoded on a wide range of distance scales, ranging from tens of bases to megabases. We developed a multiscale framework to analyze and visualize the information content of genomic signals. Different types of signals, such as G+C content or DNA methylation, are characterized by distinct patterns of signal enrichment or depletion across scales spanning several orders of magnitude. These patterns are associated with a variety of genomic annotations. By integrating the information across all scales, we demonstrated improved prediction of gene expression from polymerase II chromatin immunoprecipitation sequencing (ChIP-seq) measurements, and we observed that gene expression differences in colorectal cancer are related to methylation patterns that extend beyond the single-gene scale. Our software is available at https://github.com/tknijnen/msr/.
authors.affiliation: Institute for Systems Biology, Seattle, Washington, USA.
authors.forename: Theo A
authors.initials: TA
authors.lastname: Knijnenburg
authors.affiliation: 1] Seattle Biomedical Research Institute, Seattle, Washington, USA. [2].
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Ramsey
authors.affiliation: University of Southern California Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, California, USA.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Berman
authors.affiliation: Seattle Biomedical Research Institute, Seattle, Washington, USA.
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: Kennedy
authors.affiliation: Institute for Systems Biology, Seattle, Washington, USA.
authors.forename: Arian F A
authors.initials: AF
authors.lastname: Smit
authors.affiliation: 1] Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands. [2] Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.
authors.forename: Lodewyk F A
authors.initials: LF
authors.lastname: Wessels
authors.affiliation: University of Southern California Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, California, USA.
authors.forename: Peter W
authors.initials: PW
authors.lastname: Laird
authors.affiliation: Seattle Biomedical Research Institute, Seattle, Washington, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Aderem
authors.affiliation: Institute for Systems Biology, Seattle, Washington, USA.
authors.forename: Ilya
authors.initials: I
authors.lastname: Shmulevich
mesh_terms: D000818:Animals; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D023281:Genomics / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA; D012984:Software; D059467:Transcriptome
chemical_list: D004247:DNA
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