Name
Title | ||
|---|---|---|
Simultaneous Identification for Synergistic Transcription Factors and their Transcription Factor Binding Sites |
Abstract | ||
|---|---|---|
Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1109/CISIS.2011.90 | CISIS |
Keywords | Field | DocType |
significant interaction,known consensus,synergistic transcription factor,tf pair,binding motif,yeast,significant motif assignment,transcriptional regulation,coregulated gene,binding site,genomics,transcription factor binding sites,simultaneous identification,tfs interact,corresponding tfs,synergistic transcription factors,synergistic tfs,transcription factor,saccharo-myces cerevisiae chromatin immunoprecipitation data,dna,bioinformatics,co-regulated gene,transcription factor binding site,proteins,statistical significance,transcription regulation,stress,analysis of variance,databases,chromatin immunoprecipitation,gene expression | Transcriptional regulation,Gene,DNA binding site,Computer science,Gene expression,Genomics,Saccharomyces cerevisiae,Chromatin immunoprecipitation,Bioinformatics,Computational biology,Transcription factor,Distributed computing | Conference |
ISBN | Citations | PageRank |
978-0-7695-4373-4 | 0 | 0.34 |
References | Authors | |
13 | 3 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Zing Tsung-Yeh Tsai | 1 | 1 | 0.72 |
| Grace Tzu-Wei Huang | 2 | 20 | 2.39 |
| Huai-Kuang Tsai | 3 | 132 | 14.33 |