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Table 2 Results of robustness analysis of DISCLOSE

From: DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites

Functional category

Member size

Significance frequency

In original study

GO-0006164 : purine nucleotide biosynthetic process

28

94.03%

Y

COG-F : Nucleotide transport and metabolism

84

93.56%

Y

GO-0003735 : structural constituent of ribosome

59

88.06%

Y

INT-SigB : general stress sigma factor

66

87.91%

Y

COG-J : Translation, ribosomal structure and biogenesis

161

87.12%

Y

PW-path-bsu00020 : Citrate cycle

18

86.18%

N

GO-0003723 : RNA binding

107

85.87%

Y

COG-N : Cell motility and secretion

57

85.71%

Y

INT-SigG : late forespore-specific gene expression

61

84.30%

N

PW-path-bsu00193 : ATP synthesis

8

83.04%

Y

UP-67 : Ligase

78

79.74%

Y

GO-0006935 : chemotaxis

26

73.46%

Y

UP-56 : Glycolysis

19

72.21%

Y

UP-29 : Cell division

32

71.11%

Y

PW-path-bsu00720 : Reductive carboxylate cycle

13

70.32%

N

PW-path-bsu00240 : Pyrimidine metabolism

51

68.60%

Y

PW-path-bsu00970 : Aminoacyl-tRNA biosynthesis

23

68.28%

Y

COG-L : DNA replication, recombination and repair

138

65.93%

Y

UP-15 : Threonine biosynthesis

3

58.55%

N

COG-G : Carbohydrate transport and metabolism

246

55.88%

Y

GO-0006520 : amino acid metabolic process

184

53.53%

Y

UP-124 : Sporulation

180

49.92%

Y

INT-SigK : late mother cell-specific gene expression

57

47.40%

N

PW-path-bsu03070 : Type III secretion system

9

44.27%

N

INT-PurR : negative regulation of the purine operons

10

43.32%

N

GO-0015293 : symporter activity

82

35.63%

Y

UP-25 : Porphyrin biosynthesis

13

27.62%

N

UP-179 : Folate biosynthesis

6

27.31%

N

PW-path-bsu00190 : Oxidative phosphorylation

31

26.05%

N

PW-path-bsu02060 : Phosphotransferase system (PTS)

27

24.96%

N

COG-D : Cell division and chromosome partitioning

33

24.64%

Y

GO-0008360 : regulation of cell shape

36

24.17%

Y

PW-path-bsu00740 : Ribo avin metabolism

5

23.54%

N

PW-path-bsu00030 : Pentose phosphate pathway

24

23.39%

N

GO-0009086 : methionine biosynthetic process

15

22.76%

Y

UP-17 : Hydrogen ion transport

15

21.66%

Y

INT-SigE : early mother cell-specific gene expression

82

21.66%

N

PW-path-bsu00920 : Sulfur metabolism

15

19.62%

N

INT-SigA : RNA polymerase major sigma-43 factor

320

18.52%

N

COG-O : Posttranslational modification, protein turnover, chaperones

98

17.11%

N

PW-path-bsu00400 : Phenylalanine, tyrosine and tryptophan biosynthesis

28

16.16%

N

PW-path-bsu00252 : Alanine and aspartate metabolism

21

16.01%

Y

GO-0009252 : peptidoglycan biosynthetic process

32

15.22%

Y

PW-path-bsu00260 : Glycine, serine and threonine metabolism

34

12.55%

Y

UP-84 : Fatty acid biosynthesis

11

12.55%

Y

GO-0000103 : sulfate assimilation

7

10.67%

N

GO-0000105 : histidine biosynthetic process

11

10.36%

N

PW-path-bsu00670 : One carbon pool by folate

11

10.20%

N

  1. The performance of DISCLOSE was evaluated by comparing the clustering analysis results of a time course DNA microarray experiment of Bacillus subtilis ([17]) with the results obtained by DISCLOSE. This analysis recapitulated most of the findings of the original study. In addition, several significantly overrepresented categories were found by DISCLOSE that were not discussed by the authors. The following table list the functional categories that are identified by DISCLOSE from the robustness analysis with a significance frequency of at least 10%. The last column indicates if a category was found significant in the original study. Redundant functional categories were removed from the table (e.g., functional category GO:0006096-glycolysis was not listed in the table since this functional category was already covered by a UniProt category UP:56-glycolysis). (Abbreviations used; GO : Gene Ontology, INT : Regulon, PW: metabolic pathway, UP : UniProt and COG : Clusters of Orthologous Gtroups)