Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms

Jafari, Mohieddin; Mirzaie, Mehdi; Sadeghi, Mehdi

doi:10.1186/s12859-015-0755-1

Cited by 14 publications

(11 citation statements)

References 64 publications

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“…The giant component comprising 8604 DEG products was selected for further analysis. Given the high false-positive rate in PPINs (Jafari et al, 2013, 2015), the topological overlap matrix (TOM)-based adjacency function was used to filter the effect of spurious or weak connections (Li and Horvath, 2007; Yip and Horvath, 2007). Proteins encoded by the 61 seed genes were identified in the refined global PPIN for neighborhood analysis.…”

Section: Resultsmentioning

confidence: 99%

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways

et al. 2016

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The prototypical neurotropic virus, rabies, is a member of the Rhabdoviridae family that causes lethal encephalomyelitis. Although there have been a plethora of studies investigating the etiological mechanism of the rabies virus and many precautionary methods have been implemented to avert the disease outbreak over the last century, the disease has surprisingly no definite remedy at its late stages. The psychological symptoms and the underlying etiology, as well as the rare survival rate from rabies encephalitis, has still remained a mystery. We, therefore, undertook a systems biomedicine approach to identify the network of gene products implicated in rabies. This was done by meta-analyzing whole-transcriptome microarray datasets of the CNS infected by strain CVS-11, and integrating them with interactome data using computational and statistical methods. We first determined the differentially expressed genes (DEGs) in each study and horizontally integrated the results at the mRNA and microRNA levels separately. A total of 61 seed genes involved in signal propagation system were obtained by means of unifying mRNA and microRNA detected integrated DEGs. We then reconstructed a refined protein–protein interaction network (PPIN) of infected cells to elucidate the rabies-implicated signal transduction network (RISN). To validate our findings, we confirmed differential expression of randomly selected genes in the network using Real-time PCR. In conclusion, the identification of seed genes and their network neighborhood within the refined PPIN can be useful for demonstrating signaling pathways including interferon circumvent, toward proliferation and survival, and neuropathological clue, explaining the intricate underlying molecular neuropathology of rabies infection and thus rendered a molecular framework for predicting potential drug targets.

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Section: Resultsmentioning

confidence: 99%

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways

et al. 2016

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“…Predicted protein-protein interactors of HvTHF1 were inferred using interlogs (32,35). Orthologs of HvThf1 with Arabidopsis thaliana, Zea mays and Oryza sativa were obtained using the Plant Compara tables from Ensembl Plants (46).…”

Section: Determination Of Interlogsmentioning

confidence: 99%

“…We analyzed the prey fragment peptide to identify the interacting domains and we found it contains a thylakoid formation protein domain. To position HvTHF1 in a signaling context we predicted protein-protein interactors using interlogs(32)(33)(34)(35). As illustrated inFig 4C, we found 18predicted interactions with four main protein families: Homeobox protein BEL1, DOF zinc finger protein, protein kinase, receptor kinase and leucin-rich receptor-like kinase.…”

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confidence: 96%

Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data

Velásquez-Zapata

Elmore

Banerjee

et al. 2020

Preprint

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Interactomes embody one of the most effective representations of cellular behavior by revealing function through protein associations. In order to build these models at the organism scale, highthroughput techniques are required to identify interacting pairs of proteins. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate protein-protein interaction networks in any organism. However, challenges remain to mining reliable information from these screens and thus, limit its broader implementation. Here, we describe a statistical framework, designated Y2HSCORES, for analyzing high-throughput Y2H screens that considers key aspects of experimental design, normalization, and controls. Three quantitative ranking scores were implemented to identify interacting partners, comprising: 1) significant enrichment under selection for positive interactions, 2) degree of interaction specificity among multi-bait comparisons, and 3) selection of in-frame interactors. Using simulation and an empirical dataset, we provide a quantitative assessment to predict interacting partners under a wide range of experimental scenarios, facilitating independent confirmation by one-to-one bait-prey tests. Simulation of Y2H-NGIS identified conditions that maximize detection of true interactors, which can be achieved with protocols such as prey library normalization, maintenance of larger culture volumes and replication of experimental treatments. Y2H-SCORES can be implemented in different yeastbased interaction screenings, accelerating the biological interpretation of experimental results. Proof-of-concept was demonstrated by discovery and validation of a novel interaction between the barley powdery mildew effector, AVRA13, with the vesicle-mediated thylakoid membrane biogenesis protein, HvTHF1.

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“…Given the high false-positive rate in PPINs (Jafari et al, 2013b;Jafari et al, 2015), the topological overlap matrix (TOM)-based adjacency function was used to filter the effect of spurious or weak connections (Li and Horvath, 2007;Yip and Horvath, 2007). Proteins encoded by the 61 seed genes were identified in the refined global PPIN for neighborhood analysis.…”

Section: Shortest Path-based Scoring Allows Identification Of Seed Gementioning

confidence: 99%

Systems Biomedicine of Rabies Delineates the Affected Signaling pathways

Jamalkandi

Pourbadie

Mirzaie

et al. 2016

Preprint

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The prototypical neurotropic virus, rabies, is a member of the Rhabdoviridae family that causes lethal encephalomyelitis. Although there have been a plethora of studies investigating the etiological mechanism of the rabies virus and many precautionary methods have been implemented to avert the disease outbreak over the last century, the disease has surprisingly no definite remedy at its late stages. The psychological symptoms and the underlying etiology, as well as the rare survival rate from rabies encephalitis, has still remained a mystery. We, therefore, undertook a systems biomedicine approach to identify the network of gene products implicated in rabies. This was done by meta-analyzing whole-transcriptome microarray datasets of the CNS infected by strain CVS-11, and integrating them with interactome data using computational and statistical methods. We first determined the differentially expressed genes (DEGs) in each study and horizontally integrated the results at the mRNA and microRNA levels separately. A total of 61 seed genes involved in signal propagation system were obtained by means of unifying mRNA and microRNA detected integrated DEGs. We then reconstructed a refined protein-protein interaction network (PPIN) of infected cells to elucidate biological signaling transduction pathways affected by rabies virus. To validate our findings, we confirmed differential expression of randomly selected genes in the network using Real-time PCR. In conclusion, the identification of seed genes and their network neighborhood within the refined PPIN can be useful for demonstrating signaling pathways including interferon circumvent, toward proliferation and survival, and neuropathological clue, explaining the intricate underlying molecular neuropathology of rabies infection and thus rendered a molecular framework for predicting potential drug targets.

show abstract

Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms

Cited by 14 publications

References 64 publications

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways

Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data

Systems Biomedicine of Rabies Delineates the Affected Signaling pathways

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