Computational Systems Biology Methods and Protocols.7z

Table 3(continued)Method

Level of omics

Biological purpose

Mutation mRNA miRNA Modification Protein Metabolite Network Annotation

“Semi-supervised

normalizationpipelines” [

100

]

✓✓✓✓✓

Training predictive cell models based on

integrated data sources

“Integrative

computationalpipeline” [

97

]

✓✓✓

Dissecting the transcription factors (TFs)

responsible for altered miRNAexpression

“Data-driven

discovery” [

95

]

✓✓

Data-driven discovery of pain gene

candidates

“Layers of

regulation” [

99

]

✓✓

Adaptive mechanisms include

posttranscriptional andposttranslational events

pRSEM [

96

]

✓✓

Estimating relative isoform abundances

SPIA [

94

]

✓✓

Pan-cancer analysis on pathways

118 Xiang-Tian Yu and Tao Zeng