Changes

<p><b>Functional Orphans Characteristics in E. coli&nbsp;</b></p>

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<p>Translation seem to occur for the genes lacking annotation into bona fide proteins as their corresponding transcripts were not obviously (p &frac14; 0.36) less stable than the products of annotated genes (Figure 1C). Nonetheless, some differences were clear with side of their biophysical attributes and evolutionary scope associated with annotated genes. Just 21 orphans about 1.5% are necessary for viability under regular laboratory conditions worthily. In contrast with the 280 annotated genes (10%) formerly considered must-have. The orphans were also obviously less sufficient at the protein and transcript levels, and that is major characteristic of the orphans. In addition, they prefer to encode 44% of smaller with fewer domain assignments than for 74% of annotated proteins according to the SUPERFAMILY database [34]. Using a maximum-score E-value cutoff of 1 3 106 for BLAST bidirectional best hits (BDBHs), orphans also overall find less orthologs in a nonredundant dataset, filtered at 90% similarity based on the frequency of shared orthologs (Figure 1G), with an average of 0.22 as compared with 0.48 for annotated genes. However, in metagenomes, more various sequence comparisons available against current one (Figure 1H) indicated that orphan homologs (one-way BLAST hits) are distributed in diverse conditions (PLS2, S2). With all of these things, that claims the functional importance of the orphans is more than the annotations as a result.</p>

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<p><b>Overall analysis of K-12 system</b></p>

<p>Figure2 is outline of System biology studies based on PI, GC in this paper. Figure 2-a is scheme of construction of a physical network based on protein copurification and detection.&nbsp;Figure2-b is scheme of integration of four Genomic context methods.</p>

<p>First method is gene fusions which represent similarity of functionality [35,36], second method is similarity of Phylogenetic profiles [33,37-38], third method is evolutionary conservation of gene order which is direction that proteins are expressed [39-41], fourth method is measurement of intergenic distances which are close the more functionality is similar[42-44]. Figure2-c is scheme of integration of PI and GC probabilistic networks and function prediction based on Figure2-a or Figure2-b. So this group used &ldquo;StepPLR&rdquo; which is designed new integrated network topology-based method.</p>

<p>[44] Snel B, Bork P, Huynen MA (2002) The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA 99: 5890&ndash;5895.</p>

<div>[45]&nbsp;<span style="color: rgb(34, 34, 34); font-family: Arial, sans-serif; font-size: 13px; line-height: 16.1200008392334px;">Hu, P., Janga, S. C., Babu, M., D&iacute;az-Mej&iacute;a, J. J., Butland, G., Yang, W., ... &amp; Emili, A. (2009). Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.&nbsp;</span><i style="color: rgb(34, 34, 34); font-family: Arial, sans-serif; font-size: 13px; line-height: 16.1200008392334px;">PLoS biology</i><span style="color: rgb(34, 34, 34); font-family: Arial, sans-serif; font-size: 13px; line-height: 16.1200008392334px;">,&nbsp;</span><i style="color: rgb(34, 34, 34); font-family: Arial, sans-serif; font-size: 13px; line-height: 16.1200008392334px;">7</i><span style="color: rgb(34, 34, 34); font-family: Arial, sans-serif; font-size: 13px; line-height: 16.1200008392334px;">(4), 929.</span></div>