Table 2.
Statistical and bioinformatics analyses performed in published articles in the leishmaniasis field that employed RNA-seq and proteomics techniques.
| Authors | Year | DOI | Statistical methods | Enrichment analysis methods | Network-based method |
|---|---|---|---|---|---|
| RNA-seq | |||||
| Alcolea et al., 2018 | 2018 | 10.1016/j.parint.2018.03.008 | Geneious | – | – |
| Osman et al., 2017 | 2017 | 10.1371/journal.pntd.0005527 | edgeR | Ingenuity Pathway Analysis, GSEA | – |
| Masoudzadeh et al., 2017 | 2017 | 10.1016/j.actatropica.2017.08.016 | edgeR | Gene Ontology website, GSEA | – |
| Aoki et al., 2017 | 2017 | 10.1371/journal.pntd.0006026 | t-test on FPKM-values estimated by Cufflinks | Performed list-based enrichment analysis using KEGG as database without specifying tool. | – |
| Iantorno et al., 2017 | 2017 | 10.1128/mBio.01393-17 | edgeR | – | – |
| Cuypers et al., 2017 | 2017 | 10.1038/s41598-017-03987-0 | DESeq2 | BiNGO, GSEA | – |
| Fernandes et al., 2016 | 2016 | 10.1128/mBio.00027-16 | Voom/limma | ConsensusPathDB, Goseq | – |
| Christensen et al., 2016 | 2016 | 10.1371/journal.pntd.0004992 | Voom/limma | GSEA | WGCNA |
| Dillon et al., 2015 | 2015 | 10.1093/nar/gkv656 | Voom/limma | ConsensusPathDB, Goseq | – |
| Willis et al., 2014 | 2014 | 10.4049/jimmunol.1303216 | Voom/limma | – | – |
| Maretti-Mira et al., 2012 | 2012 | 10.1371/journal.pntd.0001816 | CuffDiff | Ingenuity Pathway Analysis | – |
| PROTEOMICS | |||||
| Menezes et al., 2013 | 2013 | 10.1016/j.micinf.2013.04.005 | Sequest algorithm within Bioworks software | Ingenuity Pathway Analysis | Ingenuity Pathway Analysis |
| Singh et al., 2015 | 2015 | 10.1128/IAI.02833-14 | ProteinPilot | Gene Ontology | – |
| Goldman-Pinkovich et al., 2016 | 2016 | 10.1371/journal.ppat.1005494 | Proteome Discoverer; MaxQuant | – | – |
–, did not perform.