title: A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha.
abstract: BACKGROUND
  To detect and select patterns of transcription factor binding sites (TFBSs) which distinguish genes directly regulated by estrogen receptor-alpha (ERalpha), we developed an innovative mixture model-based discriminate analysis for identifying ordered TFBS pairs.
  
  
  RESULTS
  Biologically, our proposed new algorithm clearly suggests that TFBSs are not randomly distributed within ERalpha target promoters (P-value < 0.001). The up-regulated targets significantly (P-value < 0.01) possess TFBS pairs, (DBP, MYC), (DBP, MYC/MAX heterodimer), (DBP, USF2) and (DBP, MYOGENIN); and down-regulated ERalpha target genes significantly (P-value < 0.01) possess TFBS pairs, such as (DBP, c-ETS1-68), (DBP, USF2) and (DBP, MYOGENIN). Statistically, our proposed mixture model-based discriminate analysis can simultaneously perform TFBS pattern recognition, TFBS pattern selection, and target class prediction; such integrative power cannot be achieved by current methods.
  
  
  BACKGROUND
  The software is available on request from the authors.
  
  
  BACKGROUND
  lali@iupui.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Division of Biostatistics, Department of Medicine, Indiana University School of Medicine Indianapolis, IN 47405, USA. lali@iupui.edu
authors.forename: Lang
authors.initials: L
authors.lastname: Li
authors.forename: Alfred S L
authors.initials: AS
authors.lastname: Cheng
authors.forename: Victor X
authors.initials: VX
authors.lastname: Jin
authors.forename: Henry H
authors.initials: HH
authors.lastname: Paik
authors.forename: Meiyun
authors.initials: M
authors.lastname: Fan
authors.forename: Xiaoman
authors.initials: X
authors.lastname: Li
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: Jason
authors.initials: J
authors.lastname: Robarge
authors.forename: Curtis
authors.initials: C
authors.lastname: Balch
authors.forename: Ramana V
authors.initials: RV
authors.lastname: Davuluri
authors.forename: Sun
authors.initials: S
authors.lastname: Kim
authors.forename: Tim H-M
authors.initials: TH
authors.lastname: Huang
authors.forename: Kenneth P
authors.initials: KP
authors.lastname: Nephew
mesh_terms: D000465:Algorithms; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D016002:Discriminant Analysis; D047628:Estrogen Receptor alpha / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation / Q000235:genetics*; D008956:Models, Chemical; D008957:Models, Genetic; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D047628:Estrogen Receptor alpha; D014157:Transcription Factors