The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze,
transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression
data and static or dynamic transcription factor-gene interaction data (e.g. ChIP-seq data), and
produces as output a dynamic regulatory map.
The dynamic regulatory map highlights major bifurcation events in the time series expression data
and transcription factors potentially responsible for them. See the manual and papers below for more
DREM 2.0 was released and supports a number of new features including (see manual for details):
new static binding data for mouse, human, D. melanogaster, A. thaliana
a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input
expression levels of TFs can be used to improve the models learned by DREM
the motif finder DECOD can be used in conjunction with DREM and help find DNA motifs for unannotated splits
new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations
The DREM method was originally described and applied to yeast in the paper:
J. Ernst, O. Vainas, C.T. Harbison, I. Simon, and Z. Bar-Joseph.
Reconstructing Dynamic Regulatory Maps.
Nature-EMBO Molecular Systems Biology, 3:74, 2007. Click
here for Supporting Information
specific to that paper
Short Primer: Starting DREM
1. To run DREM Java 1.5 or higher must be installed
2. Save the drem.zip file to a computer.
3. Unzip the drem.zip file
4a. If on windows double click on the .cmd file
corresponding to the condition of interest to see
DREM opened with the data from that condition.
4b. If not on windows start DREM from the drem directory with the command
java -mx1024M -ms512M -jar drem.jar -d [defaultfilename]
where defaultfilename is the name of the condition DREM should be
opened with. For instance to open DREM with the heat shock data type
java -mx1024M -ms512M -jar drem.jar -d defaultsHeatSample.txt
If you want to use a human dataset try java -mx1024M -ms512M -jar drem.jar -d defaultsHumanSample.txt
5. Once DREM is open press the execute button at the bottom.
6. To see only genes assigned to a certain path click on that
7. The gene table button displays the names of the genes currently
display by DREM.
8. The GO table displays a GO enrichment for all genes displayed by
Please read the provided manual to learn more about the features of DREM!
DREM extensions DREM has been extended to model additional biological settings and other types of high-throughput data. Details, code, and references can be found on the respective web pages:
mirDREM: supports the use of microRNAs in DREM allowing for dynamic models that integrate both TFs and miRNAs
SDREM: links dynamic transcriptional regulatory networks to upstream signaling pathways
MT-SDREM: multitask learning for modeling multiple conditions with SDREM
SMARTS: reconstructs and clusters multiple condition-specific transcriptional response networks