Table 3The representative approaches of bottom-up integrationMethod
Level of omicsBiological purposeMutation mRNA miRNA Modification Protein Metabolite Network Annotation“eQTL-based” [80]✓✓eQTL-based analysisTieDIE [92]✓✓✓Robust synthetize of signaling network“Network-based”[^79]✓✓✓Identification of disrupted pathways“Integrative networkanalysis” [114]✓✓✓Identifying important genetic andepigenetic features“TCGA-based”[^82-^85
]✓✓✓✓Characterizing somatic alterations“TCGA-based”[^86-^88
]✓✓✓Characterizing the genomic/epigenomiclandscape“TCGA-based”[^90,^91]✓✓✓✓✓Cancer subtypes caused by differentsubsets of genetic and epigeneticabnormalities“Generalizableframework” [81]✓✓Identifying pathogenetically relevantmutated genes“Integrativeframework” [89]✓✓✓Determining the prognostic, predictive,and therapeutic relevance of thefunctional proteome“Pan-cancerinitiative” [93]✓✓✓✓✓The Cancer Genome Atlas pan-canceranalysis projectdChip-GemiNI [98]✓✓✓Detecting feed-forward loops (FFLs) onTF-miRNA-mRNA network(continued)Integrative Analysis of Omics Big Data 117