Table 4: Online accessible tools for PPI network assembly, reevaluation, and comparison.

PurposeInputEvaluation resultsNetwork contentInternet accessibilityReferences

Program tools

PINTAResource 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 dataInternal scores, values, Bonferroni–Holm -valuesmenu: human, mouse, rat, worm
(C. elegans) and yeast P-PIN
http://www.esat.kuleuven.be/pinta/[221]
PCFamilyFinds homologous structure complexes of the query using BLASTP to search the structural template databaseQS or QS set in FASTA format -value agreement ratio941 protein complexeshttp://pcfamily.life.nctu.edu.tw[236]
BisoGenetBuild and visualize biological networks in a fast and user-friendly manner including P-PINList of identifiersNode degrees, cluster coefficients5365 human geneshttp://bio.cigb.edu.cu/bisogenet-cytoscape/[245]
DynaModIdentifies significant functional modules reflecting the change of modularity and differential expressions that are correlated with gene expression profiles under different conditionsGenome-wide expression profile -score, Bonferroni or FDR -valuesIn frame of GSEAhttp://biocondor6.kaist.ac.kr/dynamod/[241]
TORQUECross 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 subsetSeq of compared sets, query list, target P-PINThickness of the edge5430 proteins, 39 936 interactionshttp://www.cs.tau.ac.il/~bnet/torque.html[246]
NetworkBLASTIdentifies protein complexes within and across species, forming html page with links to schemes of interactions within complexes and additional graph data filesFiles with *PPI, BLPE *PPIlikelihood based density scorespecies related P-PIN
*two species
*single species
http://www.cs.tau.ac.il/~roded/networkblast.htm[234]

Databases

STRINGA database of functional interaction networks of proteins, globally integrated and scoredSearch based on gene annotationsprobabilistic confidence score>1100 completely sequenced organismshttp://string-db.org[251]
ChemProtDisease chemical biology database including chemicals and two millions chemical-protein interactions; indicates a possible formation of disease-associated protein complexesCompound and protein identifierscompilation of multiple chemical-protein annotations30 578 proteins
2227 disease-related proteins, 428 429 PPI
http://www.cbs.dtu.dk/services/ChemProt/[252]
NetAgeDatabase and network analysis tools for biogerontological research (integrity and functionality of P-PIN is under a tight epigenetic control)Tools for searching and browsingexperimental evidence about interactionsmiRNA-regulated P-PIN in age-related diseaseshttp://www.netage-project.org[253]
BioGRIDAll interactions in BioGRID are available through the Osprey visualization system, which can be used to query network organization in a user-defined fashionIntuitive graphical interfaceexperimental evidence about interactionsOver 198 000 genetic + protein interactions from six specieshttp://www.thebiogrid.org[254]
EHCOEncyclopedia of Hepatocellular Carcinoma genes Online collect, organize and compare unsorted HCC-related studiesCMSNL processing and softbots97 proteins, 47 highly interactive, 18 hubshttp://ehco.iis.sinica.edu.tw[255]
IntNetDB v1.0A database providing automatic prediction and visualization of PPI network among genes of interest; analysis includes domain-domain interactions, known gene contexts, crossvalidation, and so forthlist of query gene identifierslikelihood ratio following from Bayesian analysisconcerns 27 species contains GSP and GSN from HPRDhttp://hanlab.genetics.ac.cn/IntNetDB.htm[256]

*Independent alternatives; BLPE: BLASTP 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.