Analyze other biological networks with small number of attractors

Collective-Logic-Lab / Synthetic-RNA-maps

Creating synthetic RNA expression data to test control kernel ideas

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Analyze other biological networks with small number of attractors #4

Open bcdaniels opened 3 weeks ago

bcdaniels commented 3 weeks ago

The simplest test case for our analysis will be networks with two attractors. In the Cell Collective database, these have two attractors:

Cortical Area Development (N=5)
Cell Cycle Transcription By Coupled CDK And Network Oscillators (N=9)
Oxidative Stress Pathway (N=19)

These have three attractors:

T-LGL Survival Network 2011 Reduced Network (N=18)
Human Gonadal Sex Determination (N=19)
Mammalian Cell Cycle (N=20)

These have four attractors:

Toll Pathway Of Drosophila Signaling Pathway (N=11)
Neurotransmitter Signaling Pathway (N=16)
Iron Acquisition And Oxidative Stress Response In Aspergillus Fumigatus. (N=22)

bcdaniels commented 2 weeks ago

"Human Gonadal Sex Determination" has three attractors:

[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
[[1, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1]]
[[0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0]]

The above corresponds to genes in the following order:

['FGF9', 'SRY', 'RSPO1', 'UGR', 'WT1pKTS', 'SOX9', 'GATA4', 'PGD2', 'DMRT1', 'FOXL2', 'CBX2', 'WNT4', 'WT1mKTS', 'DKK1', 'AMH', 'CTNNB1', 'NR0B1', 'DHH', 'NR5A1']

bcdaniels commented 2 weeks ago

"Cell Cycle Transcription By Coupled CDK And Network Oscillators" and "Oxidative Stress Pathway" networks both have cyclic attractors.

bcdaniels commented 2 weeks ago

The table of information about the Cell Collective networks is available here: https://zenodo.org/records/5172898