Exact(4)
The answer to all three queries is a resounding "oui".
Discrimination among the selected genes [ 33] initially produced ~200 candidates that exhibited a significant (at least 3-fold) change in expression in all three queries (Table 3).
All three queries also yielded the same number of positive hits including genomes from other species from Enterobacteriaceae besides E. coli, including Serratia spp., Erwinia spp. and Citrobacter spp. Only 101 out of 106 dnd operons were included in the comparative analysis because the remaining dnd operons were located in the gaps of their respective draft genomes and were thus, incomplete.
Out of 4618 genes found from all three queries, 77% were reported in GeneCards and 43% in HuGE Navigator, well above the total numbers of genes added by other databases that each contributed less than 31% of the data (Table 3).
Similar(56)
In practice, the user of SFC does not have to create all three query triples but only two.
Conversely, other sets of genes were specific for the DNA-damaging agent and interacted with all three query genes under that condition.
As revealed by the network map, there was a subset of genes that interacted with all three query genes, suggesting that they play a more general role in the DNA damage response.
The distribution of the S-scores of all conditions for all three query genes were significantly different from one another, although the distributions for SLX4 and HRQ1 looked more similar to one another than to that of RTT107 (Kolmogorov-Smirnov test, two-sided, p-value < 7.8 × 10−16 for all comparisons, Figure S1D).
All nine queries provided results that corresponded correctly with the content of both databases: exactly all data that met the query criteria (no more and no less) were present in the query results.
A total of 137 sequences were retrieved; of these, 124 sequences were hit by all eight query sequences, and all 137 were hit by more than two queries.
In Alnus and Elaeagnus HSGs, about 40% of nonredundant LCR genes were scored as LCR genes for all four query strains, indicating that they were commonly absent in genomes of these strains.
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