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It is reasonable to suppose that LGI1 mediates interactions between different proteins using different surfaces in the two domains.
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Pairwise homology was performed between different protein sequences using Wilbur-Lipman algorithm, PAM 250 using the Gene Jockey II sequence analysis software.
The GO analysis can describe the protein function and the relationship between different proteins precisely, which is widely used in protein function annotation (Berardini et al. 2004).
Thus, just as sequence alignment, network alignment can be used for establishing from biological network data orthologous relationships between different proteins or phylogenetic relationships between different species [ 5– 7].
Suppressor analysis is a widely used strategy that facilitates the identification of functional relationships between different proteins.
Though the term protein species had been used earlier in the literature [3, 4], it was not clearly defined and used more in the sense of a protein complex consisting of several subunits [3] or to differentiate between different proteins (e.g. catalase and actin were two different protein species) [4].
Nature must have evolved the 'art' of molecular mimicry between RNA and proteins using different protein architectures that are functionally active in a ribosome 'machine' (Nakamura & Ito 2003).
Analysis of protein identity/similarity between different protein receptors was performed by protein alignment using clustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/). The percent identity was calculated as the number of identical amino acid residues, as indicated by "*" symbol in the Clustal output, divided by the total number of amino acid residues of the longest sequence (×100).
Bayesian Network inference There are different approaches to derive causal influences between measured proteins using Bayesian networks.
Protein interaction and functional annotation databases tend to refer to genes rather than gene products and do not differentiate between different protein isoforms15.
To our knowledge, we report here the largest microarray screening carried out so far between human and bacterial extracellular proteins using two different approaches.
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