Title | Multiscale representation of genomic signals. |
Publication Type | Journal Article |
Year of Publication | 2014 |
Authors | Knijnenburg, TA, Ramsey, SA, Berman, BP, Kennedy, KA, Smit, AFA, Wessels, LFA, Laird, PW, Aderem, A, Shmulevich, I |
Journal | Nat Methods |
Volume | 11 |
Issue | 6 |
Pagination | 689-94 |
Date Published | 2014 Jun |
ISSN | 1548-7105 |
Keywords | Animals, DNA, DNA Methylation, Genomics, Humans, Sequence Analysis, DNA, Software, Transcriptome |
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/.
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DOI | 10.1038/nmeth.2924 |
Alternate Journal | Nat Methods |
PubMed ID | 24727652 |
PubMed Central ID | PMC4040162 |
Grant List | U24 CA143882 / CA / NCI NIH HHS / United States HHSN272200700038C / / PHS HHS / United States R01HG002939 / HG / NHGRI NIH HHS / United States U19 AI100627 / AI / NIAID NIH HHS / United States R01 HG002939 / HG / NHGRI NIH HHS / United States R01AI025032 / AI / NIAID NIH HHS / United States R01 AI025032 / AI / NIAID NIH HHS / United States U54-AI54253 / AI / NIAID NIH HHS / United States U19AI100627 / AI / NIAID NIH HHS / United States HHSN272200700038C / AI / NIAID NIH HHS / United States K25HL098807 / HL / NHLBI NIH HHS / United States K25 HL098807 / HL / NHLBI NIH HHS / United States |