Tag: Dynamic Regulatory Event

DREM 2.0.4 / mirDREM – Dynamic Regulatory Events Miner

DREM 2.0.4/ mirDREM

:: DESCRIPTION

The DREM (Dynamic Regulatory Events Miner) 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-chip 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.

mirDREM supports the use of microRNAs in DREM

::DEVELOPER

 Systems Biology Group – Carnegie Mellon University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

  DREM , mirDREM

:: MORE INFORMATION

Citation

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.
Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z.
BMC Syst Biol. 2012 Aug 16;6(1):104.

MH Schulz, KV Pandit, CLL Cardenas, A Namasivayam, N Kaminsky and Z. Bar-Joseph.
Reconstructing dynamic miRNA regulated interaction networks
PNAS, August 28, 2013, doi: 10.1073/pnas.1303236110

SDREM 1.2 – Signaling and Dynamic Regulatory Events Miner

SDREM 1.2

:: DESCRIPTION

SDREM is a model which integrates static and time series data to link proteins and the pathways they regulate in these networks. SDREM uses prior information about proteins’ likelihood of involvement in a disease (e.g. from screens) to improve the quality of the predicted signaling pathways.

::DEVELOPER

 Systems Biology Group – Carnegie Mellon University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 SDREM

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i227-36. doi: 10.1093/bioinformatics/btt241.
Identifying proteins controlling key disease signaling pathways.
Gitter A1, Bar-Joseph Z.