8 A Practical Guide to Cancer Systems Biology
cancer, hence bioinformatics is critical for data analysis. Elucidation of
omics data from cancer patients and cells enhances our ability to identify
biomarkers and drug targets as well as to study the molecular mechanisms
of drugs. According to the targets, we can utilize bioinformatics to pick out
potential anti-cancer drugs. Additionally, systems biology approaches will
contribute in providing effective strategies for cancer therapy using both
single drug and combinations.
In this book, we will provide the protocols needed to generate omics
data, especially transcriptome and proteome, and tutorials that show readers
how to analyze these data using bioinformatics as well as to discover drug
candidates using docking simulation.
References
- Juan HF and Huang HC. (2012)Systems Biology:Applications in Cancer-related
Research, World Scientific Publishing, Singapore. - Gentles AJ and Gallahan D. (2011) Systems biology: Confronting the complexity of
cancer.Cancer Res.71:5961–5964. - Deutsch EW, Csordas A, Sun Zet al.(2017) The ProteomeXchange consortium in
2017:Supporting the cultural change in proteomicspublic data deposition.Nucleic
Acids Res.45:D1100–D1106. - Hsu CL, Chang HY, Chang JYet al.(2016) Unveiling MYCN regulatory networks
in neuroblastoma via integrative analysis of heterogeneous genomics data.Oncotarget
7:36293–36310. - Hu CW, Hsu CL, Wang YCet al.(2015) Temporal phosphoproteome dynamics
induced by an ATP synthase inhibitor citreoviridin. Mol. Cell Proteomics 14:
3284–3298. - Lee CH, Huang HC, and Juan HF. (2011) Reviewing ligand-based rational drug
design: The search for an ATP synthase inhibitor.Int. J. Mol. Sci.12:5304–5318. - Berg EL. (2014) Systems biology in drug discovery and development.Drug Discov.
Today19:113–125. - Huang TC, Chang HY, Hsu CHet al.(2008) Targeting therapy on breast carcinoma
by ATP synthase inhibitor aurovertin B.J. Proteome Res.7:1433–1444. - Sahu D, Hsu CL, Lin CCet al.(2016) Co-expression analysis identifies long noncoding
RNA SNHG1 as a novel predictor for event-free survival in neuroblastoma.Oncotarget
9:58022–58037. - Lin LL, Huang HC, and Juan HF. (2014) Deciphering molecular determinants of
chemotherapy in gastrointestinal malignancy using systems biology approaches.Drug
Discov. Today19:1402–1409. - Lin LL, Hsia CR, Hsu CLet al.(2015) Integrating transcriptomics and proteomics
to show that tanshinone IIA suppresses cell growth by blocking glucose metabolism
in gastric cancer cells.BMC Genomics16:41. - Lin LL, Huang HC, and Juan HF. (2012) Discovery of biomarkers for gastric cancer:
A proteomics approach.J. Proteome Res.75:3081–3097. - Chang HY, Huang HC, Huang TCet al.(2012) Ectopic ATP synthase blockade
suppresses lung adenocarcinoma growth by activating the unfolded protein response.
Cancer Res.72:4696–4706.