A Novel Framework for the Comparative Analysis of Biological Networks

Pache, Roland A.; Aloy, Patrick

doi:10.1371/journal.pone.0031220

Cited by 44 publications

(86 citation statements)

References 53 publications

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“…We tested NetAligner under different configurations and input data, including the original proteomes and homologies provided with the tool. According to our analysis NetAligner achieves the best performance when using the predict likely conserved interactions setting, together with the parameters suggested in its reference paper [16]. NetAligner extracts a bigger and more reliable set of alignments on its own dataset.…”

Section: Resultsmentioning

confidence: 89%

AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology

et al. 2012

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Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

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Section: Resultsmentioning

confidence: 89%

AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology

et al. 2012

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“…Conserved Subnetworks-To identify conserved subnetworks in the H. pylori PIM compared with other bacterial interactomes we used Netaligner (59,60) and extracted alignments with p Ͻ 0.01. We then looked for enriched GO terms to identify the role of complexes.…”

Section: Cloning Yeast Two-hybrid Screens and Pairwise Testscloningmentioning

confidence: 99%

A Second-generation Protein–Protein Interaction Network of Helicobacter pylori

Häuser

Céol

Rajagopala

et al. 2014

Molecular & Cellular Proteomics

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Helicobacter pylori infections cause gastric ulcers and play a major role in the development of gastric cancer. In 2001, the first protein interactome was published for this species, revealing over 1500 binary protein interactions resulting from 261 yeast two-hybrid screens. Here we roughly double the number of previously published interactions using an ORFeome-based, proteome-wide yeast two-hybrid screening strategy. We identified a total of 1515 protein-protein interactions, of which 1461 are new. The integration of all the interactions reported in H. pylori results in 3004 unique interactions that connect about 70% of its proteome. Excluding interactions of promiscuous proteins we derived from our new data a core network consisting of 908 interactions. We compared our data set to several other bacterial interactomes and experimentally benchmarked the conservation of interactions using 365 protein pairs (interologs) of E. coli of which one third turned out to be conserved in both species. Molecular &

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“…However, cancer is a complex disease arising from alterations in multiple pathways (biological/protein networks) [2] that have evolved to be very robust [3] and designing drugs against single proteins has yet to yield optimal clinical success [4]. As they are fundamental organizing principles of life, the removal of individual components through single protein-targeted drugs from such networks has surprisingly little functional consequence, even in pathological states of cancer.…”

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confidence: 99%

Network Pharmacology for Cancer Drug Discovery: Are We There Yet?

Azmi

2012

Future Med. Chem.

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Keywords: bioinformatics n combination cancer drug discovery n de-risking drugs n network medicine n network pharmacology n synergistic drug pairs n systems biology EditorialNetwork pharmacology for cancer drug discovery: are we there yet? "…network pharma cology has allowed for a deeper understanding of these secondary drug interactions, revealing that promiscuity often engages a synergistic combination of appropriate high-value targets in cancer cells to produce treatment success."

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A Novel Framework for the Comparative Analysis of Biological Networks

Cited by 44 publications

References 53 publications

AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology

AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology

A Second-generation Protein–Protein Interaction Network of Helicobacter pylori

Network Pharmacology for Cancer Drug Discovery: Are We There Yet?

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