Comparison of protein and gene expression studies. Interaction network diagram combining a subset of differentially expressed proteins detected in iTRAQ-MS pilot study, and gene products from two microarray-based gene expression studies investigating bortezomib resistance [29, 89]. Up-regulated (red) and down-regulated (green) proteins in the 8226/R5 cell line from each of the three studies are connected by intermediate interactors (white). Expression of DEK oncogene was observed in both iTRAQ-MS and Mulligan  studies; proteasome (prosome, macropain) 26S subunit non-ATPase 1 (PSMD1) was expressed in both iTRAQ-MS and Buzzeo  studies. Integration of the pilot proteomics data with gene expression datasets indicates complimentarity at the protein interaction and pathway level. Differentially expressed proteins (fold-change = 1.5) measured by iTRAQ-MS are shown to interact directly with a number of oncogenic signaling molecules including TP53, c-Myc, NF-kB, STAT, and PI3K, suggesting possible roles as upstream effectors or indicators of anti-apoptotic and/or tumorgenic processes. Other direct interactors of measured proteins include therapeutic targets in multiple myeloma, including PSMB5 (bortezomib), CDK2 (flavopiridol), and RRM2 (fludarabine phosphate). Protein interactions and illustration were generated with Ingenuity Pathways Analysis version 8.0-2602. Protein interactions were restricted to direct types (default selections) with the term "cancer" as a disease annotation in human/mouse/rat and in uncategorized species.