signed_biological — Signed gene regulatory and signalling networks (2010)

Description

Four signed biological networks compiled by G. Iacono, F. Ramezani, N. Soranzo and C. Altafini (2010) to measure how close biological networks are to being monotone (the equivalent of structurally balanced for signed graphs), and later used as benchmarks for computing the frustration index of signed networks by S. Aref, A. J. Mason and M. C. Wilson, who distributed them in a collection of signed networks (Aref and Wilson, 2019).

Nodes are genes or molecular species, and an undirected edge has sign $+1$ for an activating and $-1$ for an inhibiting interaction between them (the direction of the interactions is not kept). The networks are:

yeast: the transcriptional (gene regulatory) network of the yeast Saccharomyces cerevisiae, from the Yeast Proteome Database (Costanzo et al., 2001); 690 genes and 1,080 interactions.
ecoli: the transcriptional network of the bacterium Escherichia coli K-12, from RegulonDB version 5.0 (Salgado et al., 2006); 1,461 genes and 3,215 interactions.
egfr: the epidermal growth factor receptor (EGFR) signalling pathway map of Oda et al. (2005); 329 molecular species and 779 interactions.
macrophage: the molecular interaction map of a macrophage (a white blood cell) of Oda et al. ("Molecular interaction map of a macrophage", AfCS Research Reports 2(14), 2004); 678 molecular species and 1,425 interactions.

The networks have the following properties:

sign (edges): $+1$ for activation and $-1$ for inhibition.

The source files identify the nodes only by number (vertex $i$ corresponds to node $i+1$ of the source); the gene and molecule names are not given.

Tags

Biological Gene regulation Signed

Citation

G. Iacono, F. Ramezani, N. Soranzo and C. Altafini, "Determining the distance to monotonicity of a biological network: a graph-theoretical approach." IET Systems Biology 4(3), 223–235 (2010) 10.1049/iet-syb.2009.0040 Sci-Hub
S. Aref and M. C. Wilson, "Balance and frustration in signed networks." J. Complex Networks 7(2), 163–189 (2019) 10.1093/comnet/cny015 Sci-Hub
M. C. Costanzo et al., "YPD, PombePD and WormPD: model organism volumes of the BioKnowledge Library, an integrated resource for protein information." Nucleic Acids Research 29(1), 75–79 (2001) 10.1093/nar/29.1.75 Sci-Hub
H. Salgado et al., "RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions." Nucleic Acids Research 34, D394–D397 (2006) 10.1093/nar/gkj156 Sci-Hub
K. Oda, Y. Matsuoka, A. Funahashi and H. Kitano, "A comprehensive pathway map of epidermal growth factor receptor signaling." Molecular Systems Biology 1, 2005.0010 (2005) 10.1038/msb4100014 Sci-Hub
S. Aref, "Signed networks from sociology and political science, systems biology, international relations, finance, and computational chemistry." Figshare (2017) 10.6084/m9.figshare.5700832 Sci-Hub

Upstream URL OK

https://doi.org/10.6084/m9.figshare.5700832

Upstream license

Creative Commons Attribution 4.0 International (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	EPs	gt	GraphML	GML	csv
yeast	690	1,080	3.13	5.64	6.50	93.05	-0.40	0.02	15	0.96	Undirected	Unipartite	sign	3 KiB	6 KiB	6 KiB	6 KiB
ecoli	1,461	3,215	4.40	16.58	20.82	34.09	-0.35	0.01	9	0.94	Undirected	Unipartite	sign	7 KiB	17 KiB	16 KiB	14 KiB
egfr	329	779	4.74	3.61	8.49	62.08	0.03	0.24	12	0.95	Undirected	Unipartite	sign	3 KiB	5 KiB	4 KiB	4 KiB
macrophage	678	1,425	4.20	3.05	9.22	646.40	0.10	0.32	23	0.97	Undirected	Unipartite	sign	4 KiB	8 KiB	7 KiB	7 KiB