Figure 3.

Proteins differentially expressed between ESC and MN. (a) Volcano plot showing in red widely recognized neuronal markers overexpressed in MNs compared to ESCs in the minimal input preparation. q-Values were calculated using Student’s t-test, using a permutation-based false discovery rate (FDR) with a cutoff of 0.05. (b) Differentially expressed proteins have similar function enrichments in both the minimal and standard input protocols (p-value < 0.05). (c) Minimal and standard input protocols overlap in their results with respect to identification of differentially expressed proteins: significantly up- or downregulated proteins (MN vs ESC) from either preparation overlap with p = 2.070e^–192 or 7.639e^–164, respectively (hypergeometric test). There are close to no proteins shared across opposing groups (p = 0.221 and 0.191, hypergeometric test). ESC—embryonic stem cell; MN—motor neuron.