Most highly enriched terms in the “GO complete” Panther database applicable to the 276-protein set of S2 Table, with respect to a reference database comprising the merged experimental HeLa nuclear proteomes (nuc1 and nuc2, S1 Table).

Fold enrichment: Proportion of accessions with the given GO term in the 276-protein set / proportion in the 6700-member merged experimental nuclear reference proteome. Raw P-value: Raw statistical probability that the given fold-enrichment could have occurred by chance. FDR (false discovery rate): Proportion of decoy search results above raw P-value in paired target/decoy search. Terms are ranked by FDR: For “GO biological process” and GO molecular function”, all GO terms with an FDR > 1E-6 are shown. For “GO cellular component”, the threshold was 1E-10 since this was the approximate value for the GO term “nuclear part”, the compartment of origin.