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E-coli PPI specifications


Unique identifier OMICS_14655
Name E-coli PPI
Interface Web user interface
Restrictions to use None
Input data The gene or protein name.
Output data The module name, the module image and the coexpression module image.
Computer skills Basic
Stability Stable
Maintained Yes


  • Bacteria
    • Escherichia coli



  • person_outline Mohammad Ganjtabesh

Publication for E-coli PPI

E-coli PPI citations


Identification of Essential Proteins Based on Ranking Edge Weights in Protein Protein Interaction Networks

PLoS One
PMCID: 4182551
PMID: 25268881
DOI: 10.1371/journal.pone.0108716

[…] EW shows substantially better performance than NC and PeC on the E. coli PPI data (see section). Among the top 100, 200, 400 and 600 predictions, EW correctly predicts 57, 109, 172 and 221 verified essential proteins. In comparison, NC correctly predicts 35, 62, 1 […]


Quantitative Genome Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli

PLoS Genet
PMCID: 3930520
PMID: 24586182
DOI: 10.1371/journal.pgen.1004120

[…] of components within non-essential complexes (, ), suggesting that as in yeast , essential bacterial protein complexes occupy a central position within the E. coli GI network, just as they do in the E. coli PPI network . […]


Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

PLoS Genet
PMCID: 3219608
PMID: 22125496
DOI: 10.1371/journal.pgen.1002377

[…] d GenProtEC annotations. Literature curated genetic interactions were manually compiled from low-throughput experimental studies. To generate functional association networks (see and ), high-quality E. coli PPI curated in the eNET, BIND, DIP, IntAct and MPI_LIT databases were compiled; microarray based mRNA transcript profiles were downloaded from the M3D database to derive a network of co-expres […]


Discover Protein Complexes in Protein Protein Interaction Networks Using Parametric Local Modularity

BMC Bioinformatics
PMCID: 2974752
PMID: 20958996
DOI: 10.1186/1471-2105-11-521

[…] ensive optimization technique, simulated annealing, was used to maximize LQ, which is not feasible for large PPI networks such as yeast or human networks although it was proven useful for the smaller E. coli PPI network.In this paper we introduce a novel algorithm to infer protein complexes by combining a parametric local modularity measure and a greedy search strategy. We evaluate our approach on […]


Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology

BMC Bioinformatics
PMCID: 3098085
PMID: 20939873
DOI: 10.1186/1471-2105-11-505

[…] es. On the other hand, 1,192 proteins in the yeast HC PPI network were members of merged RNN clusters.We also compared different cluster centrality measures on other yeast PPI networks, as well as an E.Coli PPI network. Results from these PPI networks indicated that RNN cluster centrality and GO term clique centrality gave consistently higher precision values (Additional file , Figure S5). Additio […]


Probing the Extent of Randomness in Protein Interaction Networks

PLoS Comput Biol
PMCID: 2527968
PMID: 18769589
DOI: 10.1371/journal.pcbi.1000114

[…] ated that in PPI networks, high-degree nodes are almost always within one or two steps from each other . This characteristic is exemplified in , which contains a three-dimensional animation of the HT E. coli PPI network determined by Arifuzzaman et al. . […]

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E-coli PPI institution(s)
Department of Computer Science, School of Mathematics, Statistics, and Computer Science, University of Tehran, Tehran, Iran

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