title: Parameter space exploration within dynamic simulations of signaling networks.
abstract: We started offering an introduction to very basic aspects of molecular biology, for the reader coming from computer sciences, information technology, mathematics. Similarly we offered a minimum of information about pathways and networks in graph theory, for a reader coming from the bio-medical sector. At the crossover about the two different types of expertise, we offered some definition about Systems Biology. The core of the article deals with a Molecular Interaction Map (MIM), a network of biochemical interactions involved in a small signaling-network sub-region relevant in breast cancer. We explored robustness/sensitivity to random perturbations. It turns out that our MIM is a non-isomorphic directed graph. For non physiological directions of propagation of the signal the network is quite resistant to perturbations. The opposite happens for biologically significant directions of signal propagation. In these cases we can have no signal attenuation, and even signal amplification. Signal propagation along a given pathway is highly unidirectional, with the exception of signal-feedbacks, that again have a specific biological role and significance. In conclusion, even a relatively small network like our present MIM reveals the preponderance of specific biological functions over unspecific isomorphic behaviors. This is perhaps the consequence of hundreds of millions of years of biological evolution.
authors: DIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Universita degli Studi di Genova - Via Balbi, 5 - 16126 Genova, Italy. cristina.deambrosi@unige.it
authors: Cristina
authors: C
authors: De Ambrosi
authors: Annalisa
authors: A
authors: Barla
authors: Lorenzo
authors: L
authors: Tortolina
authors: Nicoletta
authors: N
authors: Castagnino
authors: Raffaele
authors: R
authors: Pesenti
authors: Alessandro
authors: A
authors: Verri
authors: Alberto
authors: A
authors: Ballestrero
authors: Franco
authors: F
authors: Patrone
authors: Silvio
authors: S
authors: Parodi
mesh_terms: D001943:Breast Neoplasms / Q000378:metabolism / Q000473:pathology*; D003198:Computer Simulation; D066246:ErbB Receptors / Q000378:metabolism; D048049:Extracellular Signal-Regulated MAP Kinases / Q000378:metabolism; D005260:Female; D005786:Gene Expression Regulation; D006801:Humans; D020935:MAP Kinase Signaling System; D008433:Mathematics; D008954:Models, Biological; D009696:Nucleic Acids / Q000378:metabolism; D011506:Proteins / Q000502:physiology; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D049490:Systems Biology / Q000379:methods*; D051176:beta Catenin / Q000378:metabolism
chemical_list: D009696:Nucleic Acids; D011506:Proteins; D051176:beta Catenin; D066246:ErbB Receptors; D048049:Extracellular Signal-Regulated MAP Kinases