Molecular profiles to biology and pathways: a systems biology approach
Tóm tắt
Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.
Tài liệu tham khảo
Durinck S, Stawiski EW, Pavía-Jiménez A, Modrusan Z, Kapur P, Jaiswal BS, et al. Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes. Nat Genet. 2014;47:13–21.
Hammerman PS, Lawrence MS, Voet D, Jing R, Cibulskis K, Sivachenko A, et al. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012;489:519–25.
Network Cancer Genome Atlas. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61–70.
Getz G, Gabriel SB, Cibulskis K, Lander E, Sivachenko A, Sougnez C, et al. Integrated genomic characterization of endometrial carcinoma. Nature. 2013;497:67–73.
Creighton CJ, Morgan M, Gunaratne PH, Wheeler DA, Gibbs RA, Gordon Robertson A, et al. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013;499:43–9.
Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, et al. Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010;18:11–22.
Network TCGA. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330–7.
Coradini D, Boracchi P, Oriana S, Biganzoli E, Ambrogi F. Differential expression of genes involved in the epigenetic regulation of cell identity in normal human mammary cell commitment and differentiation. Chin J Cancer. 2014;33:501–10.
Liu ET, Lemberger T. Higher order structure in the cancer transcriptome and systems medicine. Mol Syst Biol. 2007;3:94.
Kleensang A, Maertens A, Rosenberg M, Fitzpatrick S, Lamb J, Auerbach S, et al. t4 workshop report: pathways of toxicity. ALTEX. 2014;31:53–61.
Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D. How to infer gene networks from expression profiles. Mol Syst Biol. 2007;3:78.
Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. 2011;144:860–3.
Doderer MS, Anguiano Z, Suresh U, Dashnamoorthy R, Bishop AJ, Chen Y. Pathway distiller–multisource biological pathway consolidation. BMC Genom. 2012;13:S18.
Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma’ayan A. Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics. 2012;28:105–11.
Wang H, Zhou X. Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models. Chin J Cancer. 2013;32:186–94.