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Cold Spring Harbor Laboratory Press, Genome Research, 11(22), p. 2262-2269, 2012

DOI: 10.1101/gr.140665.112

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Spark: A navigational paradigm for genomic data exploration

Journal article published in 2012 by Cydney B. Nielsen, Hamid Younesy, Henriette O'Geen, Xiaoqin Xu, Andrew R. Jackson, Aleksandar Milosavljevic, Ting Wang, Joseph F. Costello, Martin Hirst, Peggy J. Farnham ORCID, Steven J. M. Jones
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Biologists possess the detailed knowledge critical for extracting biological insight from genome-wide data resources, and yet they are increasingly faced with nontrivial computational analysis challenges posed by genome-scale methodologies. To lower this computational barrier, particularly in the early data exploration phases, we have developed an interactive pattern discovery and visualization approach, Spark, designed with epigenomic data in mind. Here we demonstrate Spark's ability to reveal both known and novel epigenetic signatures, including a previously unappreciated binding association between the YY1 transcription factor and the corepressor CTBP2 in human embryonic stem cells.