NPAModels

R package and data for NPA models

Introduction

This package provides a set of biological causal networks for several families. They are available for the species under consideration:

• Homo sapiens (Hs)

• Mus musculus (Mm)

Networks are classified into families that describes general biological processes such as:

• CPR: Cell Proliferation

• CST: Cell Stress

• CFA: Cell Fate

• IPN: Inflammatory Process

• TRA: Tissue Repair and Angiogenesis

Preprocessing networks

After package installation, networks are installed with no precomputed data. To make them ready to be scored using the NPA algorithm provided with the NPA package, it is recommanded to run preprocessNetworks() function from the NPAModels package. This will prepare networks for fast scoring computation.

Cell Stress network family

Oxidative Stress network

The Oxidative Stress network depicts pathways regulating cellular responses to oxidative stress, which include intracellular free radical management, cellular responses to endogenous/exogenous oxidants and anti-oxidants and the glutathione metabolism.

Xenobiotic Metabolism Response network

The Xenobiotic Metabolism Response network depicts the causal mechanisms involved in xenobiotic metabolism response, including the various environmental stressors and signaling components that regulate AHR and cytochrome p450 enzymes.

Inflammatory process network family

Epithelial Innate Immune Activation network

The Epithelial Innate Immune Activation network depicts causal mechanisms involved in aspects of the innate immune system that are initially activated in pulmonary epithelium in response to exposure.

Neutrophil Signaling network

The Neutrophil Signaling network depicts the causal mechanisms that lead to various cellular functions in neutrophils, such as polarization, extravasation, respiratory burst, response to stimuli, and chemotaxis, in response to upstream signals such as CSF3, TNF, IL8, CXCL12, F2, and FPR1.

Cell Fate network family

Apoptosis network

The Apoptosis network describes causal mechanisms in several different signaling pathways that are involved in the induction of apoptosis in response to environmental stimuli.

Cell Proliferation network family

Cell cycle network

The Cell Cycle network depicts the causal mechanisms that regulate cell cycle including canonical elements of the core machinery regulating entry and exit from the mammalian cell cycle, such as cyclins, cyclin-dependent kinases and members of the E2F family.

Jak-Stat network

The Jak Stat network depicts the causal mechanisms involved in canonical Jak Stat signaling leading to cell proliferation and components of cell cycle machinery (e.g. cyclins, CDKN1B).

Tissue Repair and Angiogenesis network family

ECM Degradation network

The Extra-cellular matrix degradation network depicts the mechanisms involved.