Table 2.
Examples of software packages for mapping phenotype-related subnetworks
| Name | Full name | Website | Description | Ref. |
|---|---|---|---|---|
| GRNInfer | Gene Regulatory Network Inference Tool | http://digbio.missouri.edu/grninfer/ | A gene regulatory network inference tool from multiple microarray data sets | 83 |
| MDCinfer | Inferring protein–protein interactions based on multi-domain Co-operation | http://intelligent.eic.osaka-sandai.ac.jp/chenen/MDCinfer.htm | PPI prediction tool based on multiple domain co-operation analysis | 85 |
| TRNInfer | Inferring transcriptional regulatory networks from high-throughput data | http://intelligent.eic.osaka-sandai.ac.jp/chenen/TRNinfer.htm | Infer direct relationships between transcription factors and target genes | 85 |
| Samo | Protein Structure Alignment tool based on Multiple Objective optimization | http://doc.aporc.org/wiki/Samo | A protein structure alignment tool based on multiple objective optimization | 86 |
| MNAligner | Molecular Network Aligner | http://doc.aporc.org/wiki/MNAligner | Alignment of molecular networks by quadratic programming | 87 |
| PTG | Parsimonious Tree-Grow method for haplotype inference | http://doc.aporc.org/wiki/PTG | Parsimonious tree-grow method for haplotype inference | 88 |
| PRNA | Protein–RNA Binding-Site Prediction | http://doc.aporc.org/wiki/PRNA | Prediction of protein–RNA binding sites by a random forest method with combined features | 89 |
| NOA | Network Ontology Analysis | http://www.aporc.org/noa/ | Collection of gene ontology tools aiming to analyse functions of gene network instead of gene list | 90 |
| DDN | Differential dependency network analysis | http://www.cbil.ece.vt.edu/software.htm | Detect statistically significant topological changes in the transcriptional networks between two biological conditions | 91 |
| WGCNA | Weighted correlation network analysis | http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA | A comprehensive collection of R functions for performing various aspects of weighted correlation network analysis patterns among genes across microarray samples | 92 |
| SurvNet | N/A | http://bioinformatics.mdanderson.org/SurvNet | A bioinformatics web app for identifying network-based biomarkers that most correlate with patient survival data | 93 |
| DiME | Disease Module Extraction | www.cs.bham.ac.uk/∽szh/DiME | A novel algorithm based on the Community Extraction criterion, to extract topological core modules from biological networks as putative disease modules | 94 |
The table displays the abbreviated name and full name of the computational programs with respective description and website. In addition, the literature reference for the resource is given.