HTRgene – Integrating Heterogenous Multiple Time-series Data to Investigate Stress Response Gene and Signaling

HTRgene

:: DESCRIPTION

HTRgene was designed for integrating analysis of multiple heterogeneous time-series gene expression data to identify response genes.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
R

:: DOWNLOAD

HTRgene

:: MORE INFORMATION

Citation

Ahn H, Jung I, Chae H, Kang D, Jung W, Kim S.
HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis.
BMC Bioinformatics. 2019 Dec 2;20(Suppl 16):588. doi: 10.1186/s12859-019-3072-2. PMID: 31787073; PMCID: PMC6886170.

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.

idFBA – Dynamic analysis of integrated Signaling, Metabolic, and Regulatory Networks

idFBA

:: DESCRIPTION

idFBA (integrated dynamic FBA) is a flux balance analysis (FBA)-based strategy that dynamically simulates cellular phenotypes arising from integrated networks.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
MatLab

:: DOWNLOAD

idFBA

:: MORE INFORMATION

Citation:

Lee, J.M., E.P. Gianchandani, J.A. Eddy, and J.A. Papin. 2008.
Dynamic analysis of integrated signaling, metabolic, and regulatory networks.
PLoS Computational Biology, 4(5): e1000086