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Table 1 Confirmed results from Prosecutor

From: Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

Organism gene functional category rank auc reference
Campylobacter jejuni Cj0391c Pathway flagellar assembly 2 0.76 [41, 42]
  Cj1242 GO:0003774 motor activity 3 0.75 [42]
  Cj1316c GO:0019861 agellum 7 0.72 [43]
Escherichia coli yncE GO:0015343 siderophore-iron transmembrane transporter activity 7 0.96 [44]
  ybiX UP:Enterobactin biosynthesis 1 0.99 [44]
  cho GO:0009432 SOS response 17 0.92 [45]
  ybeD GO:0051082 unfolded protein binding 1 0.78 [46]
  ulaC GO:0019852 L-ascorbic acid metabolic process 1 0.76 [47]
  yciW GO:0006534 cysteine metabolic process 10 0.82 [48]
Bacillus subtilis ypbG transcriptional module SigM 18 0.81 [49]
  ykuO transcriptional module Fur 8 0.75 [50]
  yviF GO:0006935 chemotaxis 37 0.90 [51]
  ylxF Pathway Flagellar assembly 7 0.89 [52]
  yfnE transcriptional module GerE 52 0.81 [53]
Streptomyces coelicolor SCBAC28G1.05 PW:Biosynthesis of type II polyketide back- bone 1 0.99 [54]
  SCBAC28G1.07 PW:Biosynthesis of type II polyketide products 8 0.76 [54]
Vibroi cholera VC1688 GO:0006826 iron ion transport 2 0.87 [55]
  VCA0216 GO:0019290 siderophore biosynthetic process 8 0.98 [55]
  VC1267 GO:0019290 siderophore biosynthetic process 6 0.98 [55]
  1. Functional predictions identified by Prosecutor for several organisms that are confirmed using literature information. Gene: the gene for which a validated functional prediction with a functional category (column three) was found. Rank: the position of a gene in the prioritized list based on p-values. These p-values describe the functional prediction significance for every individual gene with a specific functional category. AUC: the expression coherence value for a functional category with respect to its own members. Notice the examples of genes for which a particular annotation is assigned rank 1. This means that this gene is more close associated with this functional category then any of the original known members of the category, indicating a very high confidence in the prediction.