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pcmr12126-sup-0001-TableS1.xlsxapplication/msexcel11KTable S1. This table shows that the total number of hubs tested in each PPI network-transcriptome evaluation varied due to differences in curating of PPI interactions as well as the different platforms and processing methods used to generate each gene expression dataset. This number also varied because we defined ‘hubs’ in two different ways: 1) Proteins with 5 or more direct interaction partners (k≥5); and, 2) Proteins among the top 15% of the PPI network node degree distribution. Refer to Appendix S1 for more information.
pcmr12126-sup-0002-TableS2.xlsxapplication/msexcel223KTable S2. These tables (A to D) report all significant (Punadjusted < 0.05) hubs identified in the present study, ordered by the transcriptome and PPI dataset examined as well as by the hub definition and the class (outcome or mutation) evaluated. Refer to Appendix S1 for unabridged table captions.
pcmr12126-sup-0003-TableS3.xlsxapplication/msexcel32KTable S3. These tables (A to D) report the results of gene ontology enrichment analyses for the significant hubs identified in this study. Refer to Appendix S1 for unabridged table captions.
pcmr12126-sup-0004-TableS4.xlsxapplication/msexcel89KTable S4. This table lists the hubs showing significant (Punadjusted  < 0.05) and highly reproducible differences in their correlation of gene co-expression with their interaction partners, as a function of either patient outcome or BRAF/NRAS mutation status at each of two different definitions of hub ('Methods').
pcmr12126-sup-0005-TableS5.xlsxapplication/msexcel11KTable S5. This table lists the therapeutic drug–target interactions (© 2000–2012 GeneGo Inc., MetaCore™ version 6.9 build 30881) for eight of the 32 hubs showing highly reproducible differences in their correlation of gene co-expression with their interaction partners, as a function of patient outcome ('Methods', Table 1).
pcmr12126-sup-0006-TableS6.xlsxapplication/msexcel15KTable S6. We characterized the 32 patient outcome-related hubs and the 28 mutation-associated hubs showing significant (Padjusted < 0.05) and highly reproducible differences in correlation of co-expression with their interaction partners (shown in Table S4) using gene ontology enrichment analysis.
pcmr12126-sup-0007-SupplementaryInformation.pdfapplication/PDF147KAppendix S1. Methods and results.

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