Spark: a navigational paradigm for genomic data exploration

Genome Res. 2012 Nov;22(11):2262-9. doi: 10.1101/gr.140665.112. Epub 2012 Sep 7.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alcohol Oxidoreductases / genetics
  • Alcohol Oxidoreductases / metabolism
  • Cluster Analysis
  • Co-Repressor Proteins
  • DNA Methylation
  • Embryonic Stem Cells / chemistry
  • Epigenesis, Genetic
  • Genome, Human*
  • Humans
  • Nerve Tissue Proteins / genetics
  • Nerve Tissue Proteins / metabolism
  • Search Engine*
  • Sequence Analysis, DNA / methods*
  • YY1 Transcription Factor / genetics
  • YY1 Transcription Factor / metabolism


  • Co-Repressor Proteins
  • Nerve Tissue Proteins
  • YY1 Transcription Factor
  • YY1 protein, human
  • Alcohol Oxidoreductases
  • CTBP2 protein, human