Systems Biology (Methods in Molecular Biology)

genes in a large number of HCC samples was chosen to reflect key features of genetic mutation data. Four genes (TP53 (P53), CTNN ...

these proteins were selected without any prior knowledge of their mutation propensity in cancer. Moreover, the present model gen ...

of aberration of some mutations in HCC [62] and of these, six proteins were in the core network and five were agreed with model ...

Table 5 Prediction of top mutated genes in normal hepatocyte Gene name Model result Cyclin D-CDK4/6 Loss-of-function Cyclin E-CD ...

normal liver attractor. Biologically, HNF4α, C/EBPα, and Foxa2 are liver-enriched transcription factors which regulate the syner ...

inflammation-related positive feedback loop [76]. The two activated positive feedback loops maintain HCC attractor by affecting ...

inhibiting proliferation and inflammation, and inducing “cancer cell” differentiate into hepatocytes at the same time. There are ...

network [3, 85], such manipulation can be handled by standard procedures which pose no additional conceptual issues [27, 49]. Be ...

from high-throughput data by statistics, the endogenous molecular- cellular network, quantified by dynamical system, is a more i ...

discussed the stochastic effect here. We have shown that the struc- ture of the endogenous molecular-cellular network model is s ...

within endogenous network theory. This and other recent devel- opments strongly suggest that we need to look for new directions, ...

HCC is asymmetric. We explicitly discuss the gaps between the working endogenous network of liver and real liver at each step of ...

Weinberg RA (1995) The retinoblastoma protein and cell cycle control. Cell 81:323–330 Paget S (1989) The distribution of second ...

Alberts B et al (2007) Molecular biology of the cell. Garland Science, New York Smale S, Hirsch MW, Devaney RL (2003) Different ...

Dang CV (2012) MYC on the path to cancer. Cell 149(1):22–35 Lemmon MA, Schlessinger J (2010) Cell sig- naling by receptor tyros ...

Ao P, Kwon C, Qian H (2007) On the exis- tence of potential landscape in the evolution of complex systems. Complexity 12(4):19– ...

Chapter 12 A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression Faiz M. Khan, Mehdi Sadeghi ...

Analyzing the structure of biochemical disease networks pro- vides useful information including network hubs, regulatory motifs, ...

and significantly correlated gene, miRNA and TF pairs from the patient data. Using the workflow as shown in Fig.1, we first gene ...

is organized and represented in a form of machine readable net- work, which is the formalized representation of a large number o ...