Then hypergeometric distribution was used to calculate the p value for GO and KO enrichment analyses.
Gene Ontology (GO) enrichment analyses were performed by the GOseq (R packages) based Wallenius non-central hyper-geometric distribution.
We used gene ontology (GO) [31, 32] to perform gene enrichment analyses in each cell type following ERBB2 inhibition.
All the enrichment analyses are based on hypergeometric tests with the Benjamini Hochberg approach [28] for multiple testing correction.
GO term enrichment analyses were performed as described [22].
The enrichment analyses described above were now repeated for the filtered signatures.
The corresponding cellular component enrichment analyses are shown in Tables S13 S14.
The differentially expressed genes were used for GO and KO enrichment analyses.
We performed enrichment analyses using the databases GO (Biological Process and Molecular Function) and KEGG pathways.
Genes, proteins and metabolites are linked to several identifier systems, providing information to perform enrichment analyses.
In order to test this hypothesis, we performed pathway enrichment analyses on each disease interactome independently.
