Table 3.
Downstream bioinformatics analysis software tools.
| Category | Name | Description |
|---|---|---|
| Downstream bioinformatics analysis tools | COVAIN [182] | A software for statistics, time series, and correlation network analysis. |
| CRONOS [137] | A cross-reference navigation server. | |
| GNET2 [179] | An R package for module inference of biological network. | |
| GSimp [123] | A Gibbs sampler-based left-censored missing value imputation approach for metabolomics studies. | |
| HIPPIE v2.0 [181] | A tool for enhancing meaningfulness and reliability of protein–protein interaction networks. | |
| IKAP [175] | A heuristic framework for inference of kinase activities from phosphoproteomics data. | |
| INGA [143] | A tool for protein function prediction combining interaction networks, domain assignments, and sequence similarity. | |
| KSEA [176] | A web-based tool for kinase activity inference from quantitative phosphoproteomics. | |
| Neglog [180] | Reconstruction of Human Protein–Protein Interaction Networks. | |
| Pathview [147] | An R package for pathway-based data integration and visualization. | |
| PP2A [163] | An integrated workflow for charting the human interaction proteome. | |
| ProLoc-GO [141] | Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. | |
| PSEA-Quant [149] | A Protein Set Enrichment Analysis on Label-Free and Label-Based Protein Quantification Data. | |
| viper [189] | Virtual Inference of Protein-activity by Enriched Regulon analysis. | |
| Databases and web services for downstream analysis | STRING [190] | A database for quality-controlled protein-protein association networks. |
| SIGNOR [135] | A database of causal relationships between biological entities. | |
| KEGG [148] | A disease and pathway database. | |
| PANTHER Pathway [145] | An Ontology-Based Pathway Database Coupled with Data Analysis Tools. | |
| Pathway Commons [185] | A web resource for biological pathway data. | |
| PhosphoSitePlus [134] | A comprehensive web services for post-translational modifications. | |
| PICR [136] | Reconciling protein identifiers across multiple source databases. | |
| Reactome [146] | A database of reactions, pathways, and biological processes. |