Dynamic Regulatory Events Miner (DREM)
DREM map of heat
shock response in yeast

The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize 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 details.

DREM 2.0 was released and supports a number of new features including (see manual for details):

Click here to download DREM version 2.0 (versionlog.txt)
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

Using DREM
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 path.
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 DREM

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:

The development of DREM, DREM2.0 and mirDREM was supported in part by NIH grants NO1 AI-5001, 1R01GM085022 and U01HL108642 and NSF CAREER award 0448453 to ZBJ