Spark: A navigational paradigm for genomic data exploration

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, Steven J M Jones

Research output: Contribution to journalArticle

23 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2262-2269
Number of pages8
JournalGenome Research
Volume22
Issue number11
DOIs
StatePublished - Nov 2012

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Epigenomics
YY1 Transcription Factor
Genome
Co-Repressor Proteins
Human Embryonic Stem Cells

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Nielsen, C. B., Younesy, H., O'Geen, H., Xu, X., Jackson, A. R., Milosavljevic, A., ... Jones, S. J. M. (2012). Spark: A navigational paradigm for genomic data exploration. Genome Research, 22(11), 2262-2269. https://doi.org/10.1101/gr.140665.112

Spark : A navigational paradigm for genomic data exploration. / Nielsen, Cydney B.; Younesy, Hamid; O'Geen, Henriette; Xu, Xiaoqin; Jackson, Andrew R.; Milosavljevic, Aleksandar; Wang, Ting; Costello, Joseph F.; Hirst, Martin; Farnham, Peggy J.; Jones, Steven J M.

In: Genome Research, Vol. 22, No. 11, 11.2012, p. 2262-2269.

Research output: Contribution to journalArticle

Nielsen, CB, Younesy, H, O'Geen, H, Xu, X, Jackson, AR, Milosavljevic, A, Wang, T, Costello, JF, Hirst, M, Farnham, PJ & Jones, SJM 2012, 'Spark: A navigational paradigm for genomic data exploration', Genome Research, vol. 22, no. 11, pp. 2262-2269. https://doi.org/10.1101/gr.140665.112
Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A et al. Spark: A navigational paradigm for genomic data exploration. Genome Research. 2012 Nov;22(11):2262-2269. https://doi.org/10.1101/gr.140665.112
Nielsen, Cydney B. ; Younesy, Hamid ; O'Geen, Henriette ; Xu, Xiaoqin ; Jackson, Andrew R. ; Milosavljevic, Aleksandar ; Wang, Ting ; Costello, Joseph F. ; Hirst, Martin ; Farnham, Peggy J. ; Jones, Steven J M. / Spark : A navigational paradigm for genomic data exploration. In: Genome Research. 2012 ; Vol. 22, No. 11. pp. 2262-2269.
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