Table 2.
Published multi-omics Integration studies using penalization methods (a partial list).
| Method | Formulation | Data | Package |
|---|---|---|---|
| Sparse CCA [66] | PMD + L1 penalty PMD + fused LASSO |
comparative genomic hybridization (CGH) data | PMA |
| Sparse mCCA [26] | CCA criteria + LAASO/fused LASSO | DLBCL copy number variation data | PMA |
| Sparse sCCA [26] | Modified CCA criteria + LASSO/fused LASSO | DLBCL data with gene expression and copy number variation data | PMA |
| Sparse PLS [56] | Approximate loss (F norm) + LASSO | Liver toxicity data, arabidopsis data, wine yeast data | mixOmics |
| CollRe [67] | Multiple least square loss + L1 penalty/ridge/fused LASSO | Neoadjuvant breast cancer data with gene expression and CNV | N/A |
| PCIA [71] | Co-inertia-based loss + LASSO/network penalty | NCI-60 cancer cell lines gene expression and protein abundance data | PCIA |
| iCluster [72] | Complete data loglikelihood + L1 penalty | Lung cancer gene expression and copy number data | iCluster |
| iCluster [73] | Complete data loglikelihood + L1 penalty/fused LASSO/Elastic Net | Breast cancer DNA methylation and gene expression data | iCluster |
| iCluster+ [74] | Complete data loglikelihood + L1 penalty | (1) CCLE data with copy number variation, gene expression and mutation (2) TCGA CRC data with DNA copy number promoter methylation and mRNA expression |
iClusterPlus |
| JIVE [27] | Approximation loss + L1 penalty | TCGA GBM data with gene expression and miRNA | r.JIVE |
| LRM [90] | Approximation Loss (F norm) + L1 penalty | TCGA | Github * |
| ARMI [91] | Multiple LAD loss + L1 penalty | (1) TCGA SKCM gene expression and CNV (2) TCGA LUAD gene expression and CNV |
Github * |
| remMap [92] | Least square loss + L1 penalty + L2 penalty | Breast cancer with RNA transcript level and DNA copy numbers | remMap |
| Robust network [93] | Semiparametric LAD loss + MCP + group MCP + network penalty | TCGA cutaneous melanoma gene expression and CNV | Github * |
| GST-iCluster [96] | Complete data loglikelihood + L1 penalty + approximated sparse overlapping group LASSO | (1) TCGA breast cancer mRNA, methylation and CNV (2) TCGA breast cancer mRNA and miRNA |
GSTiCluster |
| IS K-means [97] | BCSS + L1 penalty | (1) TCGA breast cancer mRNA, CNV and methylation (2) METABRIC breast cancer mRNA and CNV (3) Three leukemia transcriptomic datasets |
IS-Kmeans |
Note: * The corresponding authors’ Github webpage.