Table 4.
Online accessible tools for PPI network assembly, reevaluation, and comparison.
| Purpose | Input | Evaluation results | Network content | Internet accessibility | References | |
|---|---|---|---|---|---|---|
| Program tools | ||||||
|
| ||||||
| PINTA | Resource for the prioritization of disease related candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. | Files with disease-specific expression data | Internal scores, P values, Bonferroni–Holm P-values | menu: human, mouse, rat, worm (C. elegans) and yeast P-PIN |
http://www.esat.kuleuven.be/pinta/ | [221] |
| PCFamily | Finds homologous structure complexes of the query using BLASTP to search the structural template database | QS or QS set in FASTA format | Z-value agreement ratio | 941 protein complexes | http://pcfamily.life.nctu.edu.tw | [236] |
| BisoGenet | Build and visualize biological networks in a fast and user-friendly manner including P-PIN | List of identifiers | Node degrees, cluster coefficients | 5365 human genes | http://bio.cigb.edu.cu/bisogenet-cytoscape/ | [245] |
| DynaMod | Identifies significant functional modules reflecting the change of modularity and differential expressions that are correlated with gene expression profiles under different conditions | Genome-wide expression profile | Z-score, Bonferroni or FDR P-values | In frame of GSEA | http://biocondor6.kaist.ac.kr/dynamod/ | [241] |
| TORQUE | Cross species querying allows users to run topology-free queries on predefined or user-provided target networks resulting in subnetwork of the target network most similar to query subset | Seq of compared sets, query list, target P-PIN | Thickness of the edge | 5430 proteins, 39 936 interactions | http://www.cs.tau.ac.il/~bnet/torque.html | [246] |
| NetworkBLAST | Identifies protein complexes within and across species, forming html page with links to schemes of interactions within complexes and additional graph data files | Files with ∗PPI, BLPE ∗PPI | likelihood based density score | species related P-PIN ∗two species ∗single species |
http://www.cs.tau.ac.il/~roded/networkblast.htm | [234] |
|
| ||||||
| Databases | ||||||
|
| ||||||
| STRING | A database of functional interaction networks of proteins, globally integrated and scored | Search based on gene annotations | probabilistic confidence score | >1100 completely sequenced organisms | http://string-db.org | [251] |
| ChemProt | Disease chemical biology database including 7 × 105 chemicals and two millions chemical-protein interactions; indicates a possible formation of disease-associated protein complexes | Compound and protein identifiers | compilation of multiple chemical-protein annotations | 30 578 proteins 2227 disease-related proteins, 428 429 PPI |
http://www.cbs.dtu.dk/services/ChemProt/ | [252] |
| NetAge | Database and network analysis tools for biogerontological research (integrity and functionality of P-PIN is under a tight epigenetic control) | Tools for searching and browsing | experimental evidence about interactions | miRNA-regulated P-PIN in age-related diseases | http://www.netage-project.org | [253] |
| BioGRID | All interactions in BioGRID are available through the Osprey visualization system, which can be used to query network organization in a user-defined fashion | Intuitive graphical interface | experimental evidence about interactions | Over 198 000 genetic + protein interactions from six species | http://www.thebiogrid.org | [254] |
| EHCO | Encyclopedia of Hepatocellular Carcinoma genes Online collect, organize and compare unsorted HCC-related studies | CMS | NL processing and softbots | 97 proteins, 47 highly interactive, 18 hubs | http://ehco.iis.sinica.edu.tw | [255] |
| IntNetDB v1.0 | A database providing automatic prediction and visualization of PPI network among genes of interest; analysis includes domain-domain interactions, known gene contexts, crossvalidation, and so forth | list of query gene identifiers | likelihood ratio following from Bayesian analysis | concerns 27 species contains GSP and GSN from HPRD | http://hanlab.genetics.ac.cn/IntNetDB.htm | [256] |
∗Independent alternatives; BLPE: BLASTP E values between pairs of proteins from each of the compared species; CMS: content management system; GSEA: gene set enrichment analyses; GSP, GSN: gold standard positive and a gold standard negative dataset of HPRD, respectively; HCC: hepatocellular carcinoma; HPRD: human protein reference database; NL: natural language; PE: probabilistic evaluation; PPI: protein-protein interactions; QS: query sequences; seq: sequences.