TY - JOUR
T1 - A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-α
AU - Li, Lang
AU - Cheng, Alfred S L
AU - Jin, Victor X.
AU - Paik, Henry H.
AU - Fan, Meiyun
AU - Li, Xiaoman
AU - Zhang, Wei
AU - Robarge, Jason
AU - Balch, Curtis
AU - Davuluri, Ramana V.
AU - Kim, Sun
AU - Huang, Tim H M
AU - Nephew, Kenneth P.
N1 - Funding Information:
This research was supported by National Cancer Institute grants CA085289 (K.P.N.) and CA113001 (T.H-M.H.).
PY - 2006/9/15
Y1 - 2006/9/15
N2 - Motivation: To detect and select patterns of transcription factor binding sites (TFBSs) which distinguish genes directly regulated by estrogen receptor-α (ERα), we developed an innovative mixture model-based discriminate analysis for identifying ordered TFBS pairs. Results: Biologically, our proposed new algorithm clearly suggesTFBSs are not randomly distributed within ERα 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 ERα 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.
AB - Motivation: To detect and select patterns of transcription factor binding sites (TFBSs) which distinguish genes directly regulated by estrogen receptor-α (ERα), we developed an innovative mixture model-based discriminate analysis for identifying ordered TFBS pairs. Results: Biologically, our proposed new algorithm clearly suggesTFBSs are not randomly distributed within ERα 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 ERα 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.
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U2 - 10.1093/bioinformatics/btl329
DO - 10.1093/bioinformatics/btl329
M3 - Article
C2 - 16809387
AN - SCOPUS:33748692896
SN - 1367-4803
VL - 22
SP - 2210
EP - 2216
JO - Bioinformatics
JF - Bioinformatics
IS - 18
ER -