Non-linear dimensionality reduction of signaling networks

doi:10.1186/1752-0509-1-27

BMC Systems Biology

Volume 1

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Research article

Non-linear dimensionality reduction of signaling networks

Sergii Ivakhno¹^,2 and J Douglas Armstrong²

¹Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

²School of Informatics, 5 Forrest Hill, University of Edinburgh, Edinburgh EH1 2QL, UK

author email corresponding author email

BMC Systems Biology 2007, 1:27doi:10.1186/1752-0509-1-27


Published:	8 June 2007

Additional files

Additional file 1:

PCA projections of the Cytokine compendium and AfCS double ligand screen datasets with supplementary tables. Provides figures of PCA projections of the Cytokine compendium and AfCS double ligand screen datasets. List of measured protein signals and apoptosis markers used in the construction of the Cytokine compendium. Mean ranking of the molecular signals in the Cytokine compendium dataset obtained based on the sensitivity analysis with neural networks. List of ligands used in the AfCS double ligand screen with functional coherence scores of the clusters found using Isomap and PCA.

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Additional file 2:

The guide to the software used in the paper. provides brief description of the software that was used in the manuscript, software availability additional justification for particular parameters used

Format: DOC Size: 31KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional file 3:

Script to generate tab delimited file from raw AfCS double ligand screen dataset. Example perl script to generate tab delimited file from raw AfCS double ligand screen dataset.

Format: PL Size: 1KB Download file

Additional file 4:

Scripts for pre-processing AfCS double ligand screen dataset. Example perl script to pre-process tab delimited file of AfCS double ligand screen dataset.

Format: PL Size: 2KB Download file

Additional file 5:

Matlab script to perform classification with SVM. Example matlab script to perform classification with SVM (10 fold cross validation) in the Isomap first two components.

Format: M Size: 1KB Download file