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Table 2 List of target organisms used in the experiments.

From: A systematic study of genome context methods: calibration, normalization and combination

short name full name #gen. #w/fn. #enz. #samp. %pos weight
ECK12 Escherichia coli K-12 substr. MG1655 4496 3185 1000 495510 0.621 1.000
EC157 Escherichia coli O157:H7 EDL933 5475 1032 706 248865 1.327 0.884
ECCFT Escherichia coli CFT073 5379 721 577 166176 0.968 0.856
SHIG Shigella flexneri 2a str. 2457T 4207 886 597 177310 1.020 0.795
VCHO Vibrio cholerae O1 biovar El Tor str. N16961 3949 863 583 169653 1.244 0.528
CAULO Caulobacter crescentus CB15 3818 919 615 188805 0.964 0.362
MTBC Mycobacterium tuberculosis CDC1551 4235 760 569 161596 1.157 0.238
MTBR Mycobacterium tuberculosis H37Rv 3968 811 578 166753 1.409 0.238
FRANT Francisella tularensis tularensis SCHU S4 1671 491 317 50086 1.512 0.230
HPY Helicobacter pylori 26695 1609 415 228 25878 1.946 0.155
  1. The columns correspond to the short and full names for the organism, the total number of genes in the genome, the number of genes with some functional annotation, the number of genes that encode enzymes that catalyze small-molecule reactions, the total number of pairs of such genes (which corresponds to the number of samples used to report results, except in Sections 4.7 and for some results in Section 4.8 where all known-function genes are paired to create samples instead of just small-molecule enzymes), the proportion of positive samples among these samples, and the fraction of genes in the genome that have homologous sequences in ECK12. Organisms are sorted by this last column.