Supplementary Materials

Cytoplasmic protein aggregates interfere with nucleo-cytoplasmic transport of protein and RNA

Andreas C. Woerner, Frédéric Frottin, Daniel Hornburg, Li R. Feng, Felix Meissner, Maria Patra, Jörg Tatzelt, Matthias Mann, Konstanze F. Winklhofer, F. Ulrich Hartl, Mark S. Hipp

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S11
  • Captions for additional data tables S1 to S3
  • References
Data Table S1
Highly enriched annotations in the β17-GFP interactome in primary neurons. Results for the Fisher exact test on annotations of significant β17 interactors. Listed are annotations (Gene Ontology Biological Process (GOBP), Cellular Component (GOCC), Molecular Function (GOMF), Kyoto Encyclopedia of Genes and Genomes (KEGG)) that were significantly (FDR < 2%) enriched (enrichment factor > 2). Categories are ordered according to enrichment, which is calculated with the following equation: [(# proteins significantly enriched that belong to a certain category)*(# all proteins)]/[(# significantly enriched proteins)*(category size)]. The p-value is calculated based on a hypergeometric distribution.
Data Table S2
Annotations for individual β17 interactors present in enriched annotation categories. Ratio of low complexity sequences to complex sequences based on SEG algorithms (43), and percentage of disordered regions and longest stretch of disordered residues as predicted by IUPred-L (46). The p-value was calculated with Welch’s t test (unequal variances). To determine significantly enriched proteins for β17, we performed an S0 correction (emphasizing strength of enrichment) of 1 (42) and applied a permutation-based false discovery rate of 5 % with PERSEUS. Proteins in each category are ordered alphabetically.
Data Table S3
Complete β17-GFP interactome in primary neurons (A) Label free quantification (MaxLFQ) (40) of interaction proteomes. (B) Processed MaxLFQ data with matched annotations and t-test statistics, which is used in outlier determination. Proteins that are significantly enriched (applying a permutation based false discovery cut off at 5%, see Methods) are marked with "+" (C) Details of table headers in (A) and (B)