Pattern 6 (representing a feed-forward loop with an additional bidirectional interaction) was found only in the stress-response network with six occurrences, which is too few to detect significant functional enrichment or conservation measures and was thus excluded from further analysis.
Finally, the functional conservation of NvMeis was measured in the Xenopus embryo, which constitutes a well-established developmental model system for assessing Meis activities.
To measure the functional conservation of the mapped interactions, we define the semantic similarity of two mapped interactions as the average of the semantic similarities of the corresponding pairs of mapped proteins.
We determined sequence similarity between these orthologs at the protein level, as this is the most relevant measure for identifying functional conservation.
Networking versatility, which is indexed by k-core decomposition of the network, appears to be a notion properly reflecting the evolutionary adaptivity of domains, as measured by sequence and functional conservation.
Following our previous work (Shihab et al., 2013b, a, 2014), we describe a machine learning approach (called FATHMM-MKL) that integrates functional annotations from ENCODE with nucleotide-based sequence conservation measures.
Melzer is working with the government on conservation measures.
Assessment of landscape functional connectivity is increasingly important for planning landscape scale conservation measures.
The method uses a conservation measures from PFAM [ 94] Hidden Markov Models and functional information encoded through Gene Ontology terms.
At the Lausanne meeting, Jean-François Dufayard (CIRAD, Montpellier, France) presented a functional conservation score to this end, based on events and distances between two genes measured along a gene tree.
