Skip to main content

Table 1 Networks used in this study.

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

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],, 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]
  1. 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.