* Summary of supporting data files 1. 1099511s1.txt Summary of all linkages in the final network (FinalNet). There are 14 columns representing the log likelihood scores from each of the different data sets or integration steps, with the final column representing the final integrated score (higher scores are more confident). col 1 - ORF 1 col 2 - ORF 2 col 3 - log likelihood score from mRNA co-expression evidence col 4 - log likelihood score from co-citation evidence col 5 - log likelihood score from Gavin et al.(2002) col 6 - log likelihood score from Ho et al. (2002) col 7 - log likelihood score from Ito et al. (2000) col 8 - log likelihood score from phylogenetic profiling evidence col 9 - log likelihood score from gene fusion evidence col 10 - log likelihood score from DIP small scale experiments col 11 - log likelihood score from Tong et al. (2001) col 12 - log likelihood score from Tong et al. (2002) col 13 - log likelihood score from Uetz et al. (2000) col 14 - log likelihood score from IntNet (initial integrated network) col 15 - log likelihood score from ContextNet (linkages by context) col 16 - log likelihood score from FinalNet (final network) A total of 235,222 linkages with significant log likelihood score (>= ln(1.5) ~ 0.4) in the final network are presented. The confident set of interactions discussed in the paper (ConfidentNet) is composed of the top ranked 34,000 interactions. All log likelihood scores less than ln(1.5) are indicated as NA. 2. 1099511s2.txt; Fifty five clusters representing yeast functional modules at top level of hierarchy. Each cluster is annotated by its dominant MIPS protein functional category (chosen from the 12 top level MIPS categories) with its associated code number: 01 Metabolism 02 Energy 03 Cell cycle & DNA processing 04 Transcription/RNA processing/RNA transport 05 Protein synthesis 06 Protein fate 08 Cellular transport 10 Cell communication/Signal transduction 11 Cell rescue/defense 13 Regulation/integration with environment 14 Cell fate 00 Not clear Each gene is also annotated by its associated Gene Ontology (GO) biological process and cellular component annotation. 3. 1099511s3.txt Same as above but 627 clusters chosen at the level of the hierarchy with the best modularity (See explanation in supplemental methods). 4. 1099511s4.wrl Three dimensional network layout of the 18 major gene clusters (representing functional modules) out of the 54 top level clusters. This file is viewable by any VRML viewer (see below to get one of them). Here we present only the 50 strongest inter-module linkages to minimize complexity. Node size is proportional to the number of genes in the corresponding cluster and the length of an edge indicates the relative connection strength between the linked clusters (details in supplemental methods). Representative functions are presented as different node colors and shapes (see Figure 4 in the text for the legend). The numbers on nodes correspond to cluster identification numbers in yeast_54clusters.txt. 5. 1099511s5.wrl Same as above but with the 564 major clusters from the 627 cluster set. Here we also reduce complexity by presenting only the strongest 950 inter-module linkages. The numbers on nodes correspond to cluster identification numbers in yeast_627clusters.txt. * Instructions for viewing 3D network layout files (.wrl files) The files should be viewable with any VRML viewer. For example, a free Web browser plug-in 3D viewer can be downloaded from the following URL: http://www.parallelgraphics.com/products/cortona/ After installation of Cortona VRML client, simply double click wrl file. Other viewers are available from: http://www.web3d.org