Table 1.
Network diffusion based methods for the integrative analyses of multiple biological layers.
| Method | Input | Integration Level | ND | Network | Goal | Language and Availability | URLs | |
|---|---|---|---|---|---|---|---|---|
| Type | Application | |||||||
| Dmfind (Bersanelli et al., 2016b) |
gene mutations | single omics | RWR | ND-first | A priori | module detection | R package for download | https://www.itb.cnr.it/web/bioinformatics/dmfind |
| EMDN (Ma et al., 2017a) |
DNA methylation, gene expression | multiple omics | RWR | ND-first | Inferred | module detection | R package for download | https://github.com/william0701/EMDN |
| EPU (Yang et al., 2014) |
gene expression, PPI, gene ontology, gene-phenotype association data and phenotype similarity network | multiple networks | RWR | ND-first | Mixed | gene prioritization | – | – |
| GeneMANIA (Mostafavi et al., 2008) |
co-expression, PPI, genetic interaction, co-localization, shared protein domains | multiple networks | RWR | ND-first | A priori | function prediciton | Web server | http://apps.cytoscape.org/apps/genemania |
| Mashup (Cho et al., 2016) |
PPI | multiple networks | RWR | ND-first | A priori | function prediciton | Matlab code for download | http://cb.csail.mit.edu/cb/mashup/ |
| M – module (Ma et al., 2014) |
gene mutation, gene expression | multiple omics | RWR | ND-first | Inferred | module detection | R package for download | http://tanlab4generegulation.org/software/ |
| mND (Di Nanni et al., 2020) |
gene mutation, gene expression | single omics, multiple omics | RWR | ND-first | A priori | gene prioritization | R package for download | https://www.itb.cnr.it/web/bioinformatics/mnd |
| NetBag (Wu et al., 2015) |
gene expression | single omics | RWR | ND-first | A priori | disease subtyping | – | – |
| NetICS (Dimitrakopoulos et al., 2018) |
aberration events, gene expression | multiple omics | IHM | ND-first | A priori | gene prioritization | Matlab code for download | https://github.com/cbg-ethz/netics |
| NBS (Hofree et al., 2013) |
gene mutations | single omics | RWR | ND-first | A priori | disease subtyping | Matlab code for download | http://chianti.ucsd.edu/~mhofree/NBS/ |
| NBS2 (Zhang et al., 2018) |
gene mutations | single omics | RWR | ND-first | Mixed | disease subtyping | Phyton package for download | https://github.com/wzhang1984/NBSS |
| RegNet (Seifert and Beyer, 2017) |
CNV, gene expression | multiple omics | RW | ND-after | Inferred | gene prioritization | R package for download | https://github.com/seifemi/regNet |
| Ruffalo et al. (2015) | gene mutations, gene expression | multiple omics | RWR | ND-first | A priori | gene prioritization | – | – |
| Shi et al. (2016) | gene mutations, gene expression | multiple omics | RW | ND-first | Mixed | gene prioritization | – | – |
| SRF (Le Van et al., 2016) |
gene mutations, gene expression | multiple omics | RWR | ND-first | A priori | disease subtyping | Java code for download | https://github.com/rankmatrixfactorisation/SRF |
| SNF (Wang et al., 2014) |
DNA methylation, gene expression | multiple omics | DK | ND-during | Inferred | survival prediction, disease subtyping | R and Matlab code for downloads | http://compbio.cs.toronto.edu/SNF/SNF/Software.html |
| stSVM (Cun and Fröhlich, 2013) |
gene expression (mRNA, miRNA) | multiple omics | DK | ND-after | A priori | gene prioritization, survival prediction | R package for download | https://www.rdocumentation.org/packages/netClass/versions/1.2.1 |
| TieDie (Paull et al., 2013) |
gene mutations, gene expression | multiple omics | IHM | ND-first | A priori | module detection | Python and Matlab code for downloads | https://sysbiowiki.soe.ucsc.edu/tiedie |
| WSNF (Xu et al., 2016) |
gene expression (mRNA, miRNA) | multiple omics | DK | ND-during | Inferred | survival prediction, disease subtyping | R package for download | http://nugget.unisa.edu.au/Thuc/cancersubtypes |
RWR, random walk with restart; DK, diffusion kernel; IHM, insulated heat model; RW, random walk; CNV, copy number variations; PPI, Protein-Protein interaction network.