Proteomic analysis of Cul5^fl/flVavCre LSK cells. (A) Gene set enrichment analysis (GSEA) was performed and “signal-to-noise ratio” statistics were used to rank proteins identified as characteristic of stem-like MkP²¹ according to their correlation with either Cul5^fl/fl or Cul5^fl/flVavCre LSK cells. The graph below represents the ranked, ordered, nonredundant list of proteins; those on the far left (red) show a higher correlation with Cul5^fl/flVavCre LSK cells, whereas those on the far right (blue) correlated the most with Cul5^fl/fl samples. The vertical black lines indicate the position of each protein of the studied set in the ordered, nonredundant data set. The green curve corresponds to the ES (enrichment score) curve, which is the running sum of the weighted enrichment score obtained from GSEA software. (B) Volcano plot showing statistical significance (−log₁₀ adjusted P value) vs magnitude of protein expression changes (log₂ fold change) from a comparison of Cul5^fl/flVavCre LSK cells with Cul5^fl/fl controls. Overlaid are proteins significantly enriched in a previously published set of proteins identified as characteristic of stem-like MkP ²¹ that were enriched (green) or suppressed (red) in the proteome of Cul5^fl/flVavCre cells compared with Cul5^fl/fl controls; the top 10 of these exhibiting the greatest fold-change enrichment in Cul5^fl/flVavCre LSK cells are labeled. (C) Enrichment or suppression of proteins associated with inflammatory or interferon responses as well as selected pathways associated with stem cell regulation in the proteome of Cul5^fl/flVavCre compared with Cul5^fl/fl controls. The gene sets used in this comparison are provided in supplemental Table 7; pathways activated or suppressed with adjusted P value <.1 are shown. NES, normalised enrichment score; ROS, reactive oxygen species.