Systems Biology (Methods in Molecular Biology)

2.1.2 Representation of a Sub-/system Mapping out the interactions among biochemical entities as a network provides a platform f ...

been developed to infer biochemical networks from high- throughput data [18, 19]. Despite their importance, these techni- ques f ...

with critical interactions that might be critical for specific phenotype. The network-based approach with the aim of getting ins ...

2.3 Network Analysis After gathering and managing information regarding biological systems in the form of interactions networks, ...

coherent or in-coherent depending on the parity of negative links in the loop. FFL is coherent (Fig.5a) if the parity is even an ...

The network structure analysis revealed that the functioning and regulation of a network are governed by a certain set of orga- ...

formulation of new hypotheses about the effect of specific internal or external perturbations in a system [40]. Using a systems ...

few time points) and uncertain (lake of replicates and precision) [49]. Logic-based models are qualitative and do not require de ...

used when a molecule inhibits/suppresses other molecules (e.g., interaction fromX 3 toX 1 ;BF 1 ). In case of independent regula ...

model is constructed in CellNetAnalyzer, a MATLAB tool to carry out structural and dynamical analysis (here we used a logical st ...

Model simulation:Model is simulated to analyze the input-output response for normal execution of the system. The model recapitu- ...

Table 3Logical steady-state analysis of the model Input Output PTEN EGF DP1 DNA damage E2F1_proliferative_genes PT53_reg_genes E ...

composed of multiple crosstalk pathways that even contain over- lapping regulatory loops, is highly challenging. We proposed a m ...

Microarray and RNAseq are the most widely used techniques to observe the expression of gene and miRNAs in the context of various ...

3.1 Data Collection, Preprocessing, and Analysis Prostate cancer is a highly heterogeneous cancer and a leading cause of cancer ...

DEGs network using the information available on MirTarbase [92], a database for experimentally validated miRNA target genes, miR ...

metastatic integrative co-expression network is more than that of the primary integrative network which indicates that a large n ...

BCL2 role in the prostate cancer progression has not been clarified completely. There are also reports that imply association be ...

network. Downregulation of JUNB was associated with aggressive metastatic prostate cancer. Based on the previous reports the JUN ...

Based on the integrative co-expression network analysis, sur- vival analysis and literature review STAT3 may be the most signifi ...