Skip to main content

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)