dorsal/arxiv
View SchemaThe Logic Backbone of a Transcription Network
| Authors | M. Cosentino Lagomarsino, P. Jona, B. Bassetti |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0412020 |
| URL | https://arxiv.org/abs/q-bio/0412020 |
| Journal | Phys Rev Lett. 2005 Oct 7;95(15): |
Abstract
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that the logic backbone underlying all dynamic descriptions has the structure of a computational optimization problem. It involves variables, which correspond to gene expression levels, and constraints, which describe the effect of \emph{cis-}regulatory signal integration functions. In the simple paradigmatic case of Boolean variables and signal integration functions, we derive and discuss phase diagrams. Notably, the model exhibits a connectivity transition between a regime of simple, but uncertain, gene control, to a regime of complex combinatorial control.
{
"annotation_id": "d18dc725-915f-4fa7-84bb-8bca3b58e182",
"date_created": "2026-03-02T18:01:31.930000Z",
"date_modified": "2026-03-02T18:01:31.930000Z",
"file_hash": "940144124b596b1b74e1b2dcd86bffe64cfd872c4cfee2dc06f12c8ba32742b3",
"private": false,
"record": {
"abstract": "A great part of the effort in the study of coarse grained models of\ntranscription networks is directed to the analysis of their dynamical features.\nIn this letter, we consider the \\emph{equilibrium} properties of such systems,\nshowing that the logic backbone underlying all dynamic descriptions has the\nstructure of a computational optimization problem. It involves variables, which\ncorrespond to gene expression levels, and constraints, which describe the\neffect of \\emph{cis-}regulatory signal integration functions. In the simple\nparadigmatic case of Boolean variables and signal integration functions, we\nderive and discuss phase diagrams. Notably, the model exhibits a connectivity\ntransition between a regime of simple, but uncertain, gene control, to a regime\nof complex combinatorial control.",
"arxiv_id": "q-bio/0412020",
"authors": [
"M. Cosentino Lagomarsino",
"P. Jona",
"B. Bassetti"
],
"categories": [
"q-bio.MN",
"cond-mat.stat-mech",
"physics.bio-ph"
],
"journal_ref": "Phys Rev Lett. 2005 Oct 7;95(15):",
"title": "The Logic Backbone of a Transcription Network",
"url": "https://arxiv.org/abs/q-bio/0412020"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "02a31361-108f-43c5-aa2c-47d5ea1a6ea3",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}