Similar to Kelley and Ideker [1], repeat pathway pairs were removed.
Repeated pathway names were identified and amalgamated into single entities by merging the gene sets.
A consensus approach was used to review IPA's Top Networks, Top Bio Functions, Top Canonical Pathways, and Top Tox Lists for repeated pathway or ontology terms for each list of genes analyzed.
If both Frequenins have very few potentially permissive substitutions, the probability of observing repeated pathways across the subfamily should be very low.
To search for secondary effects, we removed the edges in the primary pathway, and repeated the pathway reconstruction procedure.
Recently, DinG-like proteins have been implicated in the CRISPR (clustered regularly interspaced short palindromic repeats) pathway for antiviral defence [ 32], where they appear in some bacterial lineages to have replaced Cas3, the helicase nuclease complex that unwinds and degrades RNA DNA hybrids in the final stage of viral DNA degradation [ 33].
To illustrate the consistency of the results derived from the rnor5 annotation (aforementioned) and the cross-species annotation, we repeated the pathway analysis and analyzed significantly enriched pathways (P < 0.05) between cell types in question using the cross-species annotation.
These genes may reflect the same association signal due to LD, and were therefore collapsed into one signal: when the enrichment analysis was repeated, no pathway was significantly enriched (p<0.05) in both datasets.
We repeated the pathway analysis on this list applying the same very stringent criteria used above (Bonferroni multiple test correction and p-value significant threshold of 0.01).
Finally, we also repeated our pathway analyses on the genes affected by indels in the 13 exomes, rather than on the whole set of 16 exomes, 3 of which were generated by whole-genome sequencing.
