Here are the answers to the questions:

1. What tool was used for pathway enrichment analysis?
 Metacore® was used for gene ontology localization enrichment and cell process enrichment analysis.

2. Was a tool version number provided?
 Not described.

3. What gene set library was queried (eg: GO, KEGG, Reactome or other)?
 Gene Ontology (GO) was queried.

4. Was a background gene list defined for pathway enrichment analysis?
 Not described.

5. What statistical test was used for enrichment analysis?
 Not described, but p-values were calculated and reported.

6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?
 Yes, False Discovery Rate (FDR) was reported in the tables (e.g., Table S5, Table S6, Table S7).