Conserved co-expression network

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Supplement

Supplemental tables and figures for the paper.

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Supplement

Tables from the paper

Table 1. The 12 components found in the network along with their biological enrichment. [EXCEL]

Figures from the paper

Figure 1. The expression data and procedures used to build the network.

Figure 2. Various tests to demonstrate the significance of the network.

Figure 3. Layout of the network reveals 12 highly connected components.

Figure 4. External evidence validating prediction of cell proliferation for 5 meta-genes.

Figure 5. Distribution of expression link and protein sequence conservation in the network.

Figure 6. The sizes of the meta-gene interconnections follow a power-law function.

Supplemental Tables

Table S1. The genes associated with each meta-gene from the four different organisms. [EXCEL]

Table S2. The list of experiments for each organism.

Table S3. The 5 meta-genes predicted to be involved in cell proliferation along with the meta‑genes they are connected to in the network.

Table S4. Precision of the multi-species network for connecting the 5 meta-genes with other cell proliferation genes compared to their connections in a single organism.

Table S5. The expression conservation index for each meta-gene in the network. [EXCEL]

Supplemental Figures

Figure S1. White noise analysis demonstrating the network is robust to random artifacts in the data.

Figure S2. Precision of a multi-species network built from a smaller number of experiments for connecting genes of related function compared to single species.

Figure S3. Pearson vs. Spearman rank correlation. The two measures of correlation give similar results in all four organisms.

Figure S4. Meta-genes. How meta-genes were constructed and how many genes from a single organism are contained in each.

Methods

Microarray compendia. Documents the microarray expression data included in the analysis.

Prediction of orthologous groups. Description of how meta-genes were identified.

Measuring co-expression. A discussion of the measure of correlation we used to detect co-expression.

Network construction. Computational procedure for constructing the multi-species expression network.

Network visualization and identification of components. Description of how the meta-genes were plotted and visualized on a three-dimensional landscape.

Expression conservation. Description of how conservation of expression for each meta-gene was calculated.

Random network generation. Description of how networks were constructed from permuted expression data.