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Open Access Method

The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics

Tara A Gianoulis12, Ashish Agarwal34, Michael Snyder5 and Mark B Gerstein346*

Author Affiliations

1 Department of Genetics, 77 Ave. of Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA

2 Wyss Institute for Biologically - Inspired Engineering, 3 Blackfan Circle, Boston, MA 02115, USA

3 Department of Computer Science, Yale University, 51 Prospect St, New Haven, CT 06511, USA

4 Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave, New Haven, CT 06511, USA

5 Department of Genetics, Stanford University School of Medicine, Alway M344, Stanford, CA 94305, USA

6 Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave, New Haven, CT 06511, USA

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Genome Biology 2011, 12:R32  doi:10.1186/gb-2011-12-3-r32

Published: 31 March 2011

Additional files

Additional file 1:

Supplementary materials. Further description of methods in the text and results of synthetic cross patterns.

Format: PDF Size: 405KB Download file

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Additional file 2:

Table of TF-target properties. Full listing of transcription factor and gene target properties from the regulatory network example.

Format: TXT Size: 1KB Download file

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Additional file 3:

Table of SMILES. 291 small molecules and their SMILE representations.

Format: TXT Size: 20KB Download file

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Additional file 4:

Table of molecular descriptors index. Index of all molecular descriptors calculated (only six used in main text).

Format: TXT Size: 59KB Download file

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Additional file 5:

Table of molecular descriptors values. The values for all the molecular descriptors calculated (only six used in the main text).

Format: TXT Size: 3.5MB Download file

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Additional file 6:

Table of sensitivity scores for each drug-protein treatment. Listing of the sensitivity score for each protein for each of the six molecular descriptors used in the text.

Format: TXT Size: 56KB Download file

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Additional file 7:

Summary table of the findings from the environmental stress response.

Format: PDF Size: 29KB Download file

This file can be viewed with: Adobe Acrobat Reader

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