The 2935 motifs were selected from an initial set of 4378 motifs pooled from multiple sources, including the human protein-DNA interaction database (hPDI) [43], Jaspar [44], UniPROBE [45] and TRANSFAC Professional (release 2013.4) [46] (Additional file 2).
Transcription factor target interactions were obtained from BIND (queried as protein-dna interactions), Reactome [ 22] (obtained from Pathway Commons) and NCI Pathway Interaction Database (obtained from Pathway Commons).
We obtained protein-DNA pairs involved in the three types of interactions from the nucleic acid-protein interaction database (NPIDB) [ 11].
Gao, N.L. et al. MVP: a microbe-phage interaction database.
Schaefer, C. F. et al. PID: the Pathway Interaction Database.
This motif is also involved in DNA interaction.
Two DNA interaction surfaces have been proposed.
Currently, there are several programs and databases, such as 3DNA [ 13, 14], Nucleic Acid Database (NDB) [ 15], Amino Acid-Nucleotide Interaction Database (AANT) [ 16], and Protein-Nucleic Acid Complex Database (ProNuC) [ 17], which represent previous efforts in providing some structural details of DNA or protein-DNA complex structures.
STRING is a functional interaction database that includes regulatory interactions.
Flynet is a web-accessible database of in vivo protein DNA interactions integrated with effective searching and advanced browsing capabilities.
We generated a comprehensive S. cerevisiae protein-protein and protein-DNA interaction network by combining information from the interaction databases SGD, BioGRID and BIND and recent high-throughput studies (e.g., [ 25], see our website for a complete list).
