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Table 2 Details of the reactions regulated in diauxic shift in the GLY/GNG pathway and the TCA Cycle

From: AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response

Loci ID Value ambient Module GiGA Module Diff. expressed Reactions(DeRisi)
Glycolysis/Gluconeogenesis - top      
NTH1,2, ATH1 2868 1.87 u2 u2 1
TPS1,2, TSL1, TPS3 2870 1.21 0 u2 1
GSY1,2, GLG1,2 3204 2.35 u2 u2 1
GLC3 2663 2.87 u2 u2 1
UGP1 3729 1.01 u2 0 1
GDB1 3154 2.6 u2 u2 1
PGM1,2 3518 1.56 u2 u2 1
PGI1 3160 0.48 0 0 0
GPH1 3205 0.43 u2 0 0
FBP1 3140 3.84 0 u2 1
HXK1, GLK1, HXK2 3230 0.18 0 u2 1
TCA Cycle      
PCK1 3514 3.88 u1 0 1
PYC1,2 3594 1.59 u1 0 1
PDA1,2, PDB1, LPD1, PDX1 3597 0.1 u1 0 0
ACS1,2 2785 3.7 u1 u1 1
ALD2 2860 2.25 0 0 1
CIT1 2985 2.72 u1 u1 1
ACO1 2965 2.63 u1 u1 1
IDH1,2 3286 1.49 u1 0 1
KGD1,2, LPD1 3462 2.17 u1 u1 1
LSC2 3660 0.71 u1 u1 1
SDH1,2,3,4 3658 2.53 u1 u1 1
FUM1 3142 1.89 u1 0 1
MDH1 3346 2.57 u1 u1 1
IDP2 3287 3.27 u1 u1 1
ICL1 3290 3.7 u1 u1 1
MLS1 3349 3.22 u1 u1 1
MDH2 3345 1.38 u1 0 1
GLY/GNG - TCA connection pathway      
PFK1, PFK2 3516 -1.02 d1 0 -1
FBA1 3010 -1.25 d1 0 -1
TPI1 3698 -1.12 d1 0 -1
TDH1,2,3 3182 -0.55 0 0 0
PGK1 3522 -0.51 0 0 0
GPM1 3523 -1.72 d1 0 -1
ENO1,2 3055 -1.18 d1 0 -1
PDC1,5,6 3595 -1.91 0 d1 -1
PYK1 3598 -1.81 d1 d1 -1
  1. A list of genes in central carbon metabolism that are involved in the regulated response to diauxic shift (identified in [13]) and the reactions for which they encode enzymes, along with their inferred transcriptional changes (Value, mean log fold-change). ID represents ID of the relevant reaction node in the ambient network. The final three columns represent which genes and reactions are up- or down-regulated according to ambient, GiGA and [13] (expert curation). The ambient and GiGA columns indicate which modules the reactions are in and the the Identified Reactions column shows those curated manually. ‘Diff.’ stands for ‘differentially’.