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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.