Fig. 2.
Cluster analysis of PCP-SILAC data. A, cluster analysis of protein enrichment profiles obtained from the PCP-SILAC experiment of ConA-treated cells. Three clusters were generated consisting of 238, 273, and 285 proteins, respectively, using the fuzzy c-means algorithm. Cluster A contains all identified proteins known to be associated with autophagosomes. Cluster membership values of protein enrichment profiles are indicated by the color scale. Cluster analysis of protein enrichment profiles from the PCP-SILAC experiments of HBSS- and Rapa-treated cells are shown in supplemental Fig. S2. B, Venn diagram of the cluster A proteins identified from the HBSS-, Rapa-, and ConA-treated cells. Whereas 94 proteins were in common for the three stimuli, the majority of proteins were detected by only one or two stimuli. Shown are three representative data sets of five biological replicates. C, subcellular localization of common proteins in clusters A–C based on Gene Ontology.