Tag: Microarray Dataset

GRNInfer 1.0 – Gene Regulatory Network Inference tool from multiple microarray datasets

GRNInfer 1.0

:: DESCRIPTION

GRNInfer aims to derive the most consistent network structure with respect to Multiple Microarray Datasets, by exploiting available information from a variety of experiments. Specifically, inferring gene network is formulated as an optimization problem with minimization of L1 norm for the objective function, which involves both forced matching and sparse terms. An efficient algorithm is developed to solve such a large-scale linear programming in an iterative manner. With such a procedure, a consistent and sparse structure that is also considered to be biologically plausible, can be expected to be derived.

::DEVELOPER

APORC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GRNInfer

:: MORE INFORMATION

Citation

Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen.
Inferring gene regulatory networks from multiple microarray datasets.
Bioinformatics, Vol. 22, No. 19, pp. 2413-2420, 2006.

M-align 2.8 – Align two time-series Microarray datasets using Time-warp or Gene-warp alignment matrices

M-align 2.8

:: DESCRIPTION

M-align is to align (non-linear resampling) the input data sets based on alignment matrices (*.ali files, see also Figure 7F) produced by Time-warp or Gene-warp programs. The alignment matrices can also be adjusted/generated manually with the account of E-maps. M-align takes as an input two matrices used to generate alignment matrix (*.ali) or two matrices with equivalent number of columns (time points) plus the alignment matrix (*.ali) itself.

::DEVELOPER

Dmitri Papatsenko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 M-align

:: MORE INFORMATION

Citation

Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.