Chen Lan, Cai Lun, Skogerbø Geir, Zhao Yi, Chen Runsheng
Bioinformatics Research Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
Genomics. 2008 Nov;92(5):316-21. doi: 10.1016/j.ygeno.2008.07.007. Epub 2008 Sep 16.
Ambiguously located transcription factor (TF) binding sites may introduce a large number of potentially erroneous regulatory associations into models of transcriptional regulatory networks. We have used a two-step expression similarity strategy to distinguish between likely and unlikely regulatory associations for TFs located between divergently transcribed genes in the yeast genome. Most regulatory associations of divergently transcribed genes could be assigned to either high-confidence (HC) or low-confidence (LC) groups. In support of our result, we found that most of the previously characterized regulatory associations reported in the literature fell into the HC group rather than the LC group. Moreover, genomic distance analysis showed that TF binding sites tend to be located in relative proximity to the gene that is most likely to be regulated by this TF. Finally, removal of low-confidence (i.e., most probably erroneous) regulatory associations from the transcriptional regulatory network barely affected its basic architecture.
位置不明确的转录因子（TF）结合位点可能会在转录调控网络模型中引入大量潜在的错误调控关联。我们采用了两步表达相似性策略，以区分酵母基因组中反向转录基因之间的TF可能的和不太可能的调控关联。大多数反向转录基因的调控关联可以被归为高置信度（HC）或低置信度（LC）组。为支持我们的结果，我们发现文献中报道的大多数先前已表征的调控关联属于HC组而非LC组。此外，基因组距离分析表明，TF结合位点倾向于位于最有可能受该TF调控的基因附近。最后，从转录调控网络中去除低置信度（即很可能错误的）调控关联几乎不影响其基本结构。
