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Co expression over microarray experiments, studies carried out here at
the ISB, were used to determine groups of co-regulated genes. Genes were
considered coregulated if the Pearson correlation coefficient between
the two genes was higher that 0.97 and anti-correlated if below 0.97.
These co-regulation edges are then used in combination with
chromosomal proximity edges, as described above.
Gene-fusion edges : Enright et al. (1999) have demonstrated
that domain fusions are often correlated with functional interactions
among the corresponding proteins. Domains within Halobacterium sp.
proteins fused in other genomes have been used as a measure to predict
Pylogenetic profile edges: Consistent
co-localization of pairs of conserved homologs (PCHs) across genomes
has been used as the basis for determining functional coupling genes
from an evolutionary standpoint (Overbeek et al.,
1999). These functional couplings include
proteins that may (i) participate in the same biochemical
pathway, (ii) interact with each other, and/or (iii) be
co-regulated in response to a common stimulus. To identify these
relationships we use the method of Marcotte
et al, commonly referred to as the phylogenetic profile method.
Physical interaction edges: We have mapped two-hybrid interaction maps for yeast on to Halobacterium sp. NRC-1 orthologs of yeast and Helicobacter pylori proteins as catalogued in the COG database. Possible protein binding pairs in Halobacterium sp. were inferred in a three step process: first, the COG members of binding pairs in the two hybrid maps were determined; second, all corresponding "COG partners" of the yeast and H. pylori proteins were identified in Halobacterium sp. genome; and finally, the interaction pairs were attributed a confidence level which was computed as a function of the strength of the match to the COG pair and the confidence of the two hybrid edge. In all a total of 1431interactions within the Halobacterium sp. proteome were inferred by this method.
Institute for Systems Biology
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