Recently, our own efforts investigating in vivo mediators of Acute Lymphoblastic Leukemia (ALL) have employed a data integration approach to ascertain GO biological function enrichment rather than to looking at screening targets independently (unpublished). A B-cell model of ALL was infected with a genome-scale shRNA library and after infection, cells were plated in vitro or tail-vein injected into syngeneic recipient mice. After disease developed, cells were harvested and sequenced for final shRNA representation. To analyze this data KU-55933 price we used Simultaneous Analysis of Multiple Networks (SAMNet), which is a flow-based formalism which relates

screening hits to downstream expression data using the interactome as a guide for possible connections among the data [32]. The method generated a network enriched for functional pathways, such as developmental processes, that are known to play a role in ALL – whereas these were not identified when analyzing experimental

data independently. This enrichment increases confidence that RNAi hits identified within the network are true positives. Further, SAMNet adds targets, Regorafenib clinical trial or nodes, to the network that were not present in the original high-scoring target set, making it possible to hypothesize about potential false negatives in the data. In these examples, data analysis in isolation was insufficient for discovering novel regulators and targets for therapeutic intervention. Instead, a concerted network approach, integrating multiple data sets or experimental results, improved target identification and created testable hypotheses for therapeutic development. Understanding and modulating cancer requires a concerted understanding of gene function and appreciation for each gene’s pathway membership. Much like an orchestra, the performance of the group depends on the collective group effort rather than the ability of any one player. Auditioning players individually is important for assessing skills and musicality, yet their full potential depends on their ability to contribute to the sound of the group. Gene-interference

studies are the experimental parallel of ‘auditioning’, yet their interpretation many is limited if each player is considered in isolation. Instead, the conductor must observe the player within his section to see if deficiencies affect the overall sound or if the sound of his peers compensate for his weaknesses. In the same way, building biological networks using RNAi experimental data analyzes the player in his section, and uses his pathway membership to assess his effect on the sound of the orchestra. Network Filtering’ techniques will increasingly become a secondary post-processing step to statistical analyses for gene-interference studies. We have conceptualized how network motifs may complement existing statistical approaches in Fig. 1.