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

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

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

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’.

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