Since different resources adopt different approaches to compiling protein-DNA interaction information, the combined source data were manually processed to uniformly assign Entrez gene identifiers to each participating gene and remove redundancies prior to the incorporation into TargetMine.
A user can download excel files containing protein-DNA interaction information from the TF, DNA bait and experiment pages.
First, to compare DREM 2.0 to methods that only use one type of data (clustering the expression data) we ran DREM 2.0 without using the static protein-DNA interaction information.
We propose here a hidden Markov model (HMM) to incorporate sequence motif information, TF-DNA interaction data and chromatin modification patterns to precisely identify cis-regulatory modules (CRMs).
Likewise, protein-DNA interaction data and promoter motif information have been integrated with short time series data to reconstruct the dynamic gene regulatory network of Saccharomyces cerevisiae response to stress [ 45], and to identify targets of known transcription factors in cold acclimation of Arabidopsis thaliana [ 46], respectively.
To compare to the original version of DREM we also reran the asbestos data using TF-DNA interaction data but without using the TF expression information.
This motivated our systems-based discovery framework based on the integration of gene expression, protein-protein interactions, biological process annotations and DNA-gene interaction information.
We will continue to include protein-DNA interaction data from other sources in the future, as long as precise DNA sequence information is available for interacting genomic regulatory sequences.
By considering the individual operons in each DNA bin, the interaction frequencies between operons were derived from the interaction information of DNA fragments, and their connections to the operon organization were investigated.
bZIPDB contains extensive information on human bZIP TFs, such as manually curated protein-protein and protein-DNA interactions, genomic information, synonyms, and gene ontology.
