Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks

Table 1 Networks used in this study.

Network	n	m	leaves	description
transcriptional				level of detail: functional
E.coli	1475	3320	556	gene regulatory network of the E.coli, from RegulonDB database, ([42], http://regulondb.ccg.unam.mx), version 6.3.
Yeast	690	1082	348	gene regulatory network of S.cerevisiae, from [5]
B.subtilis	918	1324	528	gene regulatory network for Bacillus Subtilis, assembled by [43]
Cory	344	366	264	Corynebacteria gene regulatory network (experimental interactions only). Assembled by [44]
signaling				level of detail: stoichiometric
EGRF	330	852	12	Epidermal Growth Factor Receptor pathway. Created by [45]
Toll-like	679	2204	59	Signaling network for the Toll-like-receptor. Assembled by [46]
metabolic				level of detail: stoichiometric
E.coli	757	6116	84	metabolic network of E.coli, from [47]
Yeast	797	4436	17	metabolic network of the yeast S.cerevisiae. Assembled from [48]

n and m are the number of nodes and edges of the directed graph; "leaves" is the number of nodes not involved in any undirected cycle. More details on the networks are provided in Tables S1-S2.

ISSN: 1752-0509