## Supplements of ISMB 2005 paper:

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Y.Yamanishi, J.-P.Vert, and M.Kanehisa,

Supervised Enzyme Network Inference from the Integration of Genomic Data and Chemical Information

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Predicted enzyme network for all the enzyme candidate proteins of the budding yeast

(1120 ORFs of Saccharomyces cerevisiae)

- Correlation coefficient matrix between the proteins in feature space (text file)

- Examples of adjacency matrix between the proteins (text file)

Note that the numbers of edges can be determined by the threshold of graphical assoications estimated.

## Data for metabolic network prediction

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Kernel matrices (668 x 668 matrices)

- Kernel matrix of gold standard metabolic network

- Kernel matrix of gene expression

- Kernel matrix of localization

- Kernel matrix of phylogenetic profiles

- Kernel matrix of chemical compatibility network

- Kernel matrix integrating all the genomic and chemical data

- Kernel matrix integrating genomic data only (to use
chemical compatibility)

- Kernel matrix by weighted integration of all the genomic and chemical data

- Kernel matrix by weighted integration of genomic data only (to use
chemical compatibility)

Note that all kernels are then normalized to 1 on the
diagonal.

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Original datasets

- ORF names of enzyme genes (668 x 1 matrix)

- ORF names and EC number list (668 x 2 matrix)

- Adjacency matrix (opposite Laplacian matrix) of enzyme genes in metabolic network in the KEGG/PATHWAY

- Adjacency matrix (opposite Laplacian matrix) of enzyme genes in chemical compatibility network based on the first 3 digits of the EC numbers

- Matrix of gene expression (668 x 157 matrix)

- Matrix of localization (668 x 23 matrix)

- Matrix of phylogenetic profiles (668 x 145 matrix)

###
Chemical datasets such as reactions and compounds used for constructing the
chemical compatibility network
(C number means Compound number in the KEGG/LIGAND below)

- ORF names and EC number list (1120 x 2 matrix)

- EC number and C number list extracted
from the compound data in the KEGG/LIGAND

- EC number and C number list (used organic compounds only) extracted
from the compound data in the KEGG/LIGAND

We removed inorganic compounds such as water, oxygen, and phosphate
based on the organic.lst made by Tonomura-san.

Note that, if there are no organic compounds involved in the EC number, "999999" is written.

- C number and EC number list extracted
from the compound data in the KEGG/LIGAND

- Adjacency matrix of EC numbers consisting of the fist 3 digits (199 x 199 matrix: if we count the label, 200 x 200 matrix)