I also found that weak interactions are important for full network connectivity (as they are linked to exclusive query-target links) while strong interactions are relevant for local fault tolerance to genetic mutations (being linked to inclusive query-target interactions, Figs. 4,5).
Currently, the Mouse Phenome Database (MPD), which includes dbSNP and Perlegen data among other resources, offers the most inclusive SNP queries for mouse strains, including comparisons of the D2 and B6 strains (see Methods for further explanation of SNP Databases).
First, one could imagine a network in which the ISs of some query-query and exclusive target-query interactions are usually strong, while the inclusive target-query ones are weak (network A, Fig. 4A).
Finally, one could consider a network in which strong ISs are mostly distributed on inclusive target-query interactions, which minimizes global efficiency (network D, Fig. 4D).
Inclusive or exclusive range queries allow matching of values between lower and upper bounds.
In this study we have presented simplified examples where the species of the query barcode is missing from reference libraries (and the entire genus for assignments to tribe and subfamily) to ensure we were solely addressing the question of assigning the query to the next least inclusive taxon.
In this case, MPD annotated the reference B6 alleles with the Perlegen data making SNP queries including the B6 strain more inclusive.
HECT amino acid sequences were retrieved with a HMMER search, using the HMM profile of the Pfam HECT domain entry (PF00632) as a query, the default parameters and an inclusive E value of 0.05.
In addition, ISs of the most inclusive target genes (hub target genes interacting with many queries) showed a distinct distribution of strong genetic interactions.
We let our Python show a bit in early versions, and made the upper bound of date range queries in the advanced interface exclusive rather than inclusive.
A confidence interval boxplot is provided within each disease comparison inclusive of every gene mapped to that pathway or GO term queried in the study, along with a link to the pathway network representation provided by KEGG.
