Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks

Table 1.

Comparison of the Results of Selected Signed Fisher Exact Test Analyses from Experiment 1

Pathway T1 T2 T3   T4   T5   T6   T7
Oxidative phosphorylation map190 1.00 1.00 0.10 0.06 0.00 0.00 0.00
Citrate cycle (TCA cycle) map20 1.00 1.00 1.00 0.05 0.03 0.00 0.00
Electron Transport System, Complex II map3150 1.00 1.00 1.00 0.02 0.00 0.00 0.00
Electron Transport System, Complex IV map3130 1.00 1.00 1.00 1.00 0.00 0.00 0.00
Pyruvate metabolism map620 1.00 1.00 0.00 0.01 0.04 0.03 0.00
Pentose phosphate cycle map30 1.00 1.00 0.07 1.00 0.03 0.00 0.00
Reductive carboxylate cycle (CO2 fixation) map720 1.00 1.00 1.00 0.06 0.12 0.00 0.00
Carbon fixation map710 1.00 1.00 0.04 0.13 0.07 0.12 0.00
Glyoxylate and dicarboxylate metabolism map630 1.00 1.00 1.00 0.11 0.05 0.07 0.00
ATP Synthase map3110 1.00 1.00 0.01 1.00 0.38 0.05 0.00
Electron Transport System, Complex III map3140 1.00 1.00 1.00 0.03 1.00 0.00 0.01
Glycolysis/Gluconeogenesis map10 1.00 1.00 0.01 0.16 0.06 0.49 0.01
Alanine and aspartate metabolism map252 1.00 1.00 0.00 0.26 0.19 −0.22 0.02
beta-Alanine metabolism map410 1.00 1.00 1.00 0.00 0.01 0.15 0.07
Glutamate metabolism map251 1.00 1.00 0.08 0.01 −0.05 −0.16 0.07
Butanoate metabolism map650 1.00 1.00 0.10 0.02 0.07 0.07 0.07
Taurine and hypotaurine metabolism map430 1.00 1.00 1.00 1.00 0.00 0.06 0.07
Prostaglandin and leukotriene metabolism map590 1.00 1.00 1.00 1.00 1.00 0.06 0.07
Fructose and mannose metabolism map51 1.00 1.00 1.00 0.03 0.59 0.53 0.09
Fatty acid metabolism map71 1.00 1.00 1.00 0.13 0.07 −0.26 −0.09
Glutathione metabolism map480 1.00 1.00 1.00 1.00 1.00 0.10 0.11
Cysteine metabolism map272 1.00 1.00 1.00 1.00 −0.01 −0.46 −0.11
Glycine, serine and threonine metabolism map260 1.00 1.00 0.17 0.43 0.07 −0.10 −0.08
Synthesis and degradation of ketone bodies map72 1.00 1.00 1.00 1.00 1.00 1.00 −0.07
Pantothenate and CoA biosynthesis map770 1.00 1.00 1.00 −0.04 −0.08 −0.15 −0.07
Valine, leucine and isoleucine biosynthesis map290 1.00 1.00 0.04 −0.11 −0.21 −0.07 −0.04
Selenoamino acid metabolism map450 1.00 1.00 1.00 1.00 0.00 −0.02 −0.01
Methionine metabolism map271 1.00 1.00 1.00 1.00 −0.01 −0.03 0.00
Aminoacryl-tRNA biosynthesis map970 1.00 1.00 1.00 1.00 1.00 0.00 0.00
RNA polymerase map3020 1.00 1.00 1.00 1.00 1.00 −0.12 0.00
Pyrimidine metabolism map240 1.00 1.00 1.00 1.00 −0.53 −0.17 0.00
Purine metabolism map230 1.00 1.00 0.01 −0.82 0.09 −0.03 0.00
Ribosome map3010 1.00 1.00 1.00 1.00 −0.99 0.00 0.00
  • (T0 vs T1) to 7 (T0T7) (T1 = 9 hours, T2 = 11 hours, T3 = 13 hours, T4 = 15 hours, T5 = 17 hours, T6 = 19 hours, T7 = 21 hours) The results have been sorted according to their ranking in the T7 column. The table shows only pathways with an absolute P-value of the Fisher exact test greater than or equal to 0.1; the complete results are reported in Supplementary material, Table 2.xls.

This Article

  1. Genome Res. 12: 1121-1126

Preprint Server