title: Spark: a navigational paradigm for genomic data exploration.
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.
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada. cydneyn@bcgsc.ca
authors.forename: Cydney B
authors.initials: CB
authors.lastname: Nielsen
authors.forename: Hamid
authors.initials: H
authors.lastname: Younesy
authors.forename: Henriette
authors.initials: H
authors.lastname: O'Geen
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Xu
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jackson
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Milosavljevic
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Costello
authors.forename: Martin
authors.initials: M
authors.lastname: Hirst
authors.forename: Peggy J
authors.initials: PJ
authors.lastname: Farnham
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D056970:Co-Repressor Proteins; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000737:chemistry; D044127:Epigenesis, Genetic; D015894:Genome, Human; D006801:Humans; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D057386:Search Engine; D017422:Sequence Analysis, DNA / Q000379:methods*; D050986:YY1 Transcription Factor / Q000235:genetics / Q000378:metabolism
chemical_list: D056970:Co-Repressor Proteins; D009419:Nerve Tissue Proteins; D050986:YY1 Transcription Factor; C494698:YY1 protein, human; D000429:Alcohol Oxidoreductases; C421248:CTBP2 protein, human