This project is dedicated to identify potentially collaborating transcription factors (TFs) for a set of co-regulated genes based on the location of their binding sites.
In higher organisms different TFs have to cooperate rather than acting individually in order to control complex genetic programs and to provide a flexible and specific gene regulation. The identification of these interactions is an important challenge for understanding the molecular mechanisms of regulating biological processes. The methodology of PC-TraFF adopts the idea of pointwise mutual information (PMI) that is originated in literature, to the field of bioinformatic by considering the genome as a document, the regulatory sequences as sentences, and TF binding sites (TFBSs) as words in order to identify collaborating TFs in a set of sequences.
Meckbach, C, Tacke, R, Hua, X, Waack, S, Wingender, E, Gültas, M (2015). PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information. BMC Bioinformatics, 16:400.
Meckbach, C, Wingender, E, Gültas, M (2018). Removing Background Co-occurrences of Transcription Factor Binding Sites Greatly Improves the Prediction of Specific Transcription Factor Cooperations. Front Genet, 9:189.