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Based on shared functional domains, MMPs can be divided into eight groups, of which five are secreted and three are membrane-bound (Egeblad and Werb, 2002).
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Briefly, the tool generates gene similarity matrices based on shared terms from 14 functional annotation sources (such as Gene Ontology).
Measuring the similarity of species based on shared gene content greatly underestimates their functional conservation.
On the other hand, a more relaxed definition of synteny based on shared gene neighborhood appears to play a functional role in vertebrate genomes [ 25, 26], and is applicable to the comparison of genomes as distant as human and hydra [ 14].
Comparing to our previous study [ 21], which used RWR algorithm on a functional similarity protein complex network built based on shared protein elements, in this study, we presented a framework to construct functional similarity protein complex networks based on not only shared protein elements, but also shared annotating GO terms and protein interactions.
In the case of the NAC transcription factor, the functional attributes appeared to be quite different in rice and wheat (Distelfeld et al. 2012) and indicated extrapolating function based on shared DNA sequence structure may not always be possible.
Therefore, we additionally constructed a functional similarity interaction between two protein complexes based on shared annotating GO terms, where a list of genes and annotating GO terms were collected from NCBI Entrez Gene FTP site (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2go.gz).
Why? Common purpose based on shared values.
We constructed a miRNA-miRNA network based on shared targets.
These relations were based on shared interests and reciprocity.
The main objective of peer support interventions is to provide functional support based on sharing of information and experience, mutual counselling and exchange among peers and this can contribute to sustained behaviour change.
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