TY - JOUR
T1 - Statistical methods for identifying yeast cell cycle transcription factors
AU - Tsai, Huai Kuang
AU - Lu, Henry Horng Shing
AU - Li, Wen Hsiung
PY - 2005/9/20
Y1 - 2005/9/20
N2 - Knowing transcription factors (TFs) involved in the yeast cell cycle is helpful for understanding the regulation of yeast cell cycle genes. We therefore developed two methods for predicting (i) individual cell cycle TFs and (ii) synergistic TF pairs. The essential idea is that genes regulated by a cell cycle TF should have higher (lower, if it is a repressor) expression levels than genes not regulated by it during one or more phases of the cell cycle. This idea can also be used to identify synergistic interactions of TFs. Applying our methods to chromatin immunoprecipitation data and microarray data, we predict 50 cell cycle TFs and 80 synergistic TF pairs, including most known cell cycle TFs and synergistic TF pairs. Using these and published results, we describe the behaviors of 50 known or inferred cell cycle TFs in each cell cycle phase in terms of activation/repression and potential positive/negative interactions between TFs. In addition to the cell cycle, our methods are also applicable to other functions.
AB - Knowing transcription factors (TFs) involved in the yeast cell cycle is helpful for understanding the regulation of yeast cell cycle genes. We therefore developed two methods for predicting (i) individual cell cycle TFs and (ii) synergistic TF pairs. The essential idea is that genes regulated by a cell cycle TF should have higher (lower, if it is a repressor) expression levels than genes not regulated by it during one or more phases of the cell cycle. This idea can also be used to identify synergistic interactions of TFs. Applying our methods to chromatin immunoprecipitation data and microarray data, we predict 50 cell cycle TFs and 80 synergistic TF pairs, including most known cell cycle TFs and synergistic TF pairs. Using these and published results, we describe the behaviors of 50 known or inferred cell cycle TFs in each cell cycle phase in terms of activation/repression and potential positive/negative interactions between TFs. In addition to the cell cycle, our methods are also applicable to other functions.
KW - Cell cycle regulators
KW - Microarray data
KW - Synergistic interactions
UR - http://www.scopus.com/inward/record.url?scp=26444501081&partnerID=8YFLogxK
U2 - 10.1073/pnas.0505874102
DO - 10.1073/pnas.0505874102
M3 - Article
C2 - 16157877
AN - SCOPUS:26444501081
SN - 0027-8424
VL - 102
SP - 13532
EP - 13537
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 38
ER -