Computational Systems Biology Methods and Protocols.7z
The Reactome [61, 62] which plays both as an archive of biological processes by modeling signal transduction, transport, DNA rep ...
e.g., an element in such tensor can reflect the expression value of one gene of the same individual at an early or latter time p ...
thousands of samples is possible nowadays because large amounts of expression data can be publicly available; however, extractin ...
Table 3The representative approaches of bottom-up integrationMethod Level of omics Biological purpose Mutation mRNA miRNA Modifi ...
Table 3(continued)Method Level of omics Biological purpose Mutation mRNA miRNA Modification Protein Metabolite Network Annotatio ...
and other omics data can be assisted to recognize the sensitive mutation by removing the passenger mutations. 1.The direct mappi ...
network consisting of druggable kinase pathways, which will be helpful for drug prioritization in individual patients [92]. 5.To ...
8.The functional influence of protein on gene regulatory. Stress responses were believed to be predominantly regulated at the tr ...
through parameters that describe the agreement among the datasets [10]. Meanwhile, a nonparametric Bayesian model has been intro ...
kernel parameters for each data type beforehand [27]. And in a biological application, the high-throughput screens for mRNA, miR ...
3.4 Tool and Visualization of Integration Currently, the academic studies not only develop the biological or computational techn ...
Table 5The representative approaches of integrative visualizationMethods Description URL ICM [ 108 ] Integrated clustering of mu ...
two-way identification of most possible TF-gene interactions: on the basis of ENCODE ChIP-Seq binding evidence or Jaspar pre- di ...
Besides, a few tools are available for general study or special application, but the platform of benchmarking the integration m ...
cancer heterogeneity based on DNA methyla- tion signature. Brief Bioinform.https://doi. org/10.1093/bib/bbw028 Voillet V, Besse ...
and subtype features by molecular data inte- gration. Bioinformatics 32(17):i445–i454. https://doi.org/10.1093/bioinformatics/ b ...
JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, ...
Xin Y, Chanrion B, O’Donnell AH, Milekic M, Costa R, Ge Y, Haghighi FG (2012) MethylomeDB: a database of DNA methylation profil ...
integrative gene expression data. Int J Data Min Bioinform 10(1):1–17 Deng M, Bragelmann J, Schultze JL, Perner S (2016) Web-TC ...
Meyerson M, Sage J, Shendure J, Schneider R, Buttner R, Wolf J, Nurnberg P, Perner S, Heukamp LC, Brindle PK, Haas S, Thomas RK ...
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