Artificial Gene Network Series Coop

Introduction

This series consists of 80 artificial gene networks. Each network consists of 100 genes with a total of 200 gene interactions (on average each gene has 2 modulators). These networks are divided in two different topologies, 40 networks are small-world and the other 40 scale-free. Additionally, while all networks follow the same kinetic type (Eq. 1), they have different values of degree of cooperativity (ie parameters ni and na):

ni = na = 1
ni = na = 2
ni = na = 4
ni = na = 8

Therefore, this series has an increasing level of cooperativity. The file names indicate the degree of cooperativity on the first number after SF or SW (the second number is just an ordinal number).

Each artificial gene network is like an in silico organism, which is used to carry out simulations of experiments. Data is available for:

null mutant experiments, where genes were deleted, one at a time, and steady-state gene expression levels are provided without noise. The tab delimited file includes the wild-type levels on the first row, followed by each of the null mutants (G1, G2, etc.) line by line. The columns represent the level of each gene (G1, G2, etc.).

Models are provided in Gepasi input files and SBML level 1 format; simulation results are supplied in tab delimited ASCII files. Models, data and network details are available in each network's summary page or within a single compressed file.

Network summary pages

Scale-free		Small-world
CoopSF1_001	null mutant data	CoopSW1_001	null mutant data
CoopSF1_002	null mutant data	CoopSW1_002	null mutant data
CoopSF1_003	null mutant data	CoopSW1_003	null mutant data
CoopSF1_004	null mutant data	CoopSW1_004	null mutant data
CoopSF1_005	null mutant data	CoopSW1_005	null mutant data
CoopSF1_006	null mutant data	CoopSW1_006	null mutant data
CoopSF1_007	null mutant data	CoopSW1_007	null mutant data
CoopSF1_008	null mutant data	CoopSW1_008	null mutant data
CoopSF1_009	null mutant data	CoopSW1_009	null mutant data
CoopSF1_010	null mutant data	CoopSW1_010	null mutant data
CoopSF2_001	null mutant data	CoopSW2_001	null mutant data
CoopSF2_002	null mutant data	CoopSW2_002	null mutant data
CoopSF2_003	null mutant data	CoopSW2_003	null mutant data
CoopSF2_004	null mutant data	CoopSW2_004	null mutant data
CoopSF2_005	null mutant data	CoopSW2_005	null mutant data
CoopSF2_006	null mutant data	CoopSW2_006	null mutant data
CoopSF2_007	null mutant data	CoopSW2_007	null mutant data
CoopSF2_008	null mutant data	CoopSW2_008	null mutant data
CoopSF2_009	null mutant data	CoopSW2_009	null mutant data
CoopSF2_010	null mutant data	CoopSW2_010	null mutant data
CoopSF4_001	null mutant data	CoopSW4_001	null mutant data
CoopSF4_002	null mutant data	CoopSW4_002	null mutant data
CoopSF4_003	null mutant data	CoopSW4_003	null mutant data
CoopSF4_004	null mutant data	CoopSW4_004	null mutant data
CoopSF4_005	null mutant data	CoopSW4_005	null mutant data
CoopSF4_006	null mutant data	CoopSW4_006	null mutant data
CoopSF4_007	null mutant data	CoopSW4_007	null mutant data
CoopSF4_008	null mutant data	CoopSW4_008	null mutant data
CoopSF4_009	null mutant data	CoopSW4_009	null mutant data
CoopSF4_010	null mutant data	CoopSW4_010	null mutant data
CoopSF8_001	null mutant data	CoopSW8_001	null mutant data
CoopSF8_002	null mutant data	CoopSW8_002	null mutant data
CoopSF8_003	null mutant data	CoopSW8_003	null mutant data
CoopSF8_004	null mutant data	CoopSW8_004	null mutant data
CoopSF8_005	null mutant data	CoopSW8_005	null mutant data
CoopSF8_006	null mutant data	CoopSW8_006	null mutant data
CoopSF8_007	null mutant data	CoopSW8_007	null mutant data
CoopSF8_008	null mutant data	CoopSW8_008	null mutant data
CoopSF8_009	null mutant data	CoopSW8_009	null mutant data
CoopSF8_010	null mutant data	CoopSW8_010	null mutant data

Download

The complete series is available in one single file: AGN-Coop.zip (8.2 Mb). This file contains all the model and data files, as well as all the HTML pages (including this one).