PMC:1794230 / 26924-29948 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1794230","sourcedb":"PMC","sourceid":"1794230","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1794230","text":"Table 2 Top 20 Predictions by PhyloScan\nC1 C2 C3 C4 C5 C6\nE. coli Sequence Fulla Fulla Reducedb Reducedb Reduced \u0026 Alignedc Reduced \u0026 Alignedc\nIndep. Species No Yes No Yes No Yes\nRank Gene log(q) Gene log(q) Gene log(q) Gene log(q) Gene log(q) Gene log(q)\n1 yibI -4.65 cdd -9.28 mtlA -5.14 mtlA -9.76 mtlA -7.66 mtlA -12.15\n2 yqcE -2.86 glpT -7.21 ygcW -2.89 cdd -9.60 yjcB -4.55 glpA -9.19\n3 b1904 -2.61 mglB -6.01 yjcB -2.62 glpA -8.31 gcd -3.99 cdd -9.16\n4 fucA -2.51 yibI -5.26 yjiY -2.60 mglB -6.53 b2146 -3.97 mglB -7.60\n5 deaD -2.51 yjiY -4.57 b2146 -2.53 gapA -5.21 fucA -3.93 udp -6.26\n6 yjiY -2.42 hemC -4.38 fucA -2.51 udp -5.17 ygcW -3.42 gapA -6.02\n7 cdd -2.29 deaD -4.35 deaD -2.47 yjiY -4.79 flhD -3.03 yjcB -5.09\n8 yeaA -2.22 ysgA -4.33 cdd -2.31 cyaA -4.70 gapA -3.03 cyaA -5.04\n9 yhcR -2.06 yhcR -3.99 gapA -2.22 deaD -4.37 ycdZ -3.01 malE -4.83\n10 ycdZ -1.96 yqcE -3.56 qseA -2.03 malE -4.29 udp -2.78 ycdZ -4.69\n11 b2736 -1.87 adhE -3.47 ycdZ -1.98 ygcW -3.63 b2248 -2.76 adhE -4.56\n12 uxaC -1.81 ycdZ -3.45 mglB -1.90 adhE -3.58 glpA -2.76 b2146 -4.53\n13 ysgA -1.77 yeaA -3.44 udp -1.86 ycdZ -3.52 mglB -2.73 fucA -4.46\n14 glpT -1.75 mlc -3.37 uxaC -1.85 mlc -3.48 qseA -2.68 pckA -4.09\n15 mglB -1.63 b1904 -3.31 glpA -1.84 fucA -3.32 pckA -2.36 aer -3.97\n16 pckA -1.39 fucA -3.23 pckA -1.45 yjcB -3.32 adhE -2.14 ygcW -3.78\n17 serA -1.23 b2736 -3.18 malE -1.36 pckA -3.23 aer -2.13 gcd -3.67\n18 aer -1.23 pckA -3.17 aer -1.32 aer -3.17 cdd -2.10 deaD -3.65\n19 adhE -1.22 aer -3.08 serA -1.32 qseA -3.07 deaD -2.04 serA -3.62\n20 mlc -1.01 yjeG -3.05 adhE -1.28 uxaC -3.07 uxaC -2.02 mlc -3.62\n# Diffs from C6 10 11 3 3 4 0\nBecause it is sometimes instructive to examine a fixed number of top hits regardless of the reported q-values, in this table we compare the six approaches' best 20 intergenic regions for Crp. By comparing each column to Column C6, which is the best approach we employed, we see that the C1-C5 approaches give significantly different q-values for, and orderings of, the predicted regulated genes. As indicated in the bottom row, the C1-C5 approaches miss several of the top-20 genes reported in C6, replacing them with genes that did not make the C6 top-20 list. In particular, although it uses all of the sequence data except S. typhi, C2 is significantly different from C6. Furthermore, although C3 has few differences from C6 in the set of genes indicated, the q-values of C3 are considerably worse and the gene order is substantially rearranged. These data suggest that the ability to simultaneously handle both aligned and unaligned data is important in obtaining accurate predictions. Notes: abcSee the caption notes for Table 1. Also see the Table 1 caption for descriptions of Columns 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