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An integrative approach for a network based meta-analysis of viral RNAi screens

Sandeep S Amberkar, Lars Kaderali
2015 Algorithms for Molecular Biology  
Results: To address this problem we propose an integrative bioinformatics pipeline that allows for a network based meta-analysis of viral high-throughput RNAi screens.  ...  Conclusions: We apply our approach to seven screens targeting three different viruses, and compare results with other published meta-analyses of viral RNAi screens.  ...  Kiani as well as two anonymous referees for useful comments and suggestions.  ... 
doi:10.1186/s13015-015-0035-7 pmid:25691914 pmcid:PMC4331137 fatcat:yr52jlxahvcg3ct5whkjtkywze

Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis

Korbinian Bösl, Aleksandr Ianevski, Thoa T. Than, Petter I. Andersen, Suvi Kuivanen, Mona Teppor, Eva Zusinaite, Uga Dumpis, Astra Vitkauskiene, Rebecca J. Cox, Hannimari Kallio-Kokko, Anders Bergqvist (+13 others)
2019 Frontiers in Immunology  
Here, we performed an integrative meta-analysis to elucidate the 17 different host-virus interactomes.  ...  Integration with functional RNA interference (RNAi) datasets showed that a large proportion of the targets are required for viral replication.  ...  ACKNOWLEDGMENTS We thank Christian Sinzger and group for the EGFP-expressing TB40E CMV strain. We thank ViroNovative and Erasmus MC for the GFP-expressing HMPV NL/1/00 strain.  ... 
doi:10.3389/fimmu.2019.02186 pmid:31636628 pmcid:PMC6787150 fatcat:vgkusfydnbarzo6sidurct5u6i

High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay

Sandeep Amberkar
2013 World Journal of Virology  
High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay.  ...  Network properties of RNAi hits identified as viral HDFs A complementary approach to integrate HT-RNAi with PPI datasets is to perform Network analyses.  ...  With the availability of several HT-RNAi screens for different viruses, a multi species meta-analysis can highlight similarities and differences between hostvirus interactions, based on RNAi screen hits  ... 
doi:10.5501/wjv.v2.i2.18 pmid:24175227 pmcid:PMC3785050 fatcat:jpltfxygnrekvhigej6phqobyu

HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings

Claire Rioualen, Quentin Da Costa, Bernard Chetrit, Emmanuelle Charafe-Jauffret, Christophe Ginestier, Ghislain Bidaut, Enrique Hernandez-Lemus
2017 PLoS ONE  
HTS-Net, a network-based analysis program, was developed to identify gene regulatory modules impacted in high-throughput screenings, by integrating transcription factors-target genes interaction data (  ...  However, there has been less development for functional analysis tools dedicated to RNAi analyses.  ...  Conclusion We are proposing the pipeline HTS-Net, a network-based RNAi analysis pipeline, for the analysis of RNAi screening data.  ... 
doi:10.1371/journal.pone.0185400 pmid:28949986 pmcid:PMC5614607 fatcat:m2njvpfherdxlbr57jqw4f7dni

Critical Nodes of Virus-Host Interaction Revealed Through an Integrated Network Analysis [article]

Korbinian Bosl, Aleksandr Ianevski, Thoa T. Than, Petter I. Andersen, Suvi Kuivanen, Mona Teppor, Eva Zusinaite, Uga Dumpis, Astra Vitkauskiene, Rebecca J. Cox, Hannimari Kallio-Kokko, Anders Bergqvist (+12 others)
2019 bioRxiv   pre-print
Here, we performed an integrative meta-analysis to elucidate the 17 different host-virus interactomes.  ...  Integration with functional RNA interference (RNAi) datasets showed that a large proportion of the targets are required for viral replication.  ...  Conflict of Interest Statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest  ... 
doi:10.1101/548909 fatcat:gk24ixh56bbbvmfnvemsuoee4y

Recent strategies and progress in identifying host factors involved in virus replication

Renate König, Silke Stertz
2015 Current Opinion in Microbiology  
At each stage of the viral life cycle an intricate interplay between virus and host takes place with the virus aiming to usurp the host cell for its purposes and the host cell trying to block the intruder  ...  In recent years these interactions have been studied on a global level by systems biology approaches, such as RNA interference screens, transcriptomic or proteomic methodologies, and exciting new insights  ...  We thank Nina Hein-Fuchs for assisting in designing the tables and together with Carsten Mü nk for critical reading of the manuscript.  ... 
doi:10.1016/j.mib.2015.06.001 pmid:26112615 pmcid:PMC7185747 fatcat:cf2hgs5b3bdsbn6wlfm7cs4hbu

Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding

Shashank Tripathi, Marie O. Pohl, Yingyao Zhou, Ariel Rodriguez-Frandsen, Guojun Wang, David A. Stein, Hong M. Moulton, Paul DeJesus, Jianwei Che, Lubbertus C.F. Mulder, Emilio Yángüez, Dario Andenmatten (+25 others)
2015 Cell Host and Microbe  
Taken together, the integrative analysis of influenza OMICs datasets illuminates a viral-host network of high-confidence human proteins that are essential for influenza A virus replication.  ...  To collectively reconcile these datasets, we performed a meta-analysis of data from eight published RNAi screens and integrated these data with three protein interaction datasets, including one generated  ...  Therefore, we performed a meta-analysis of RNAi data from eight published studies.  ... 
doi:10.1016/j.chom.2015.11.002 pmid:26651948 pmcid:PMC4829074 fatcat:lu47iwikxrdzvbi5m77tcyh2jy

The Virus–Host Interactome [chapter]

Monika Schneider, Jeffery R. Johnson, Nevan J. Krogan, Sumit K. Chanda
2016 Viral Pathogenesis  
This integrated screening and validation approach therefore yielded viral-viral and viral-host protein interaction networks.  ...  DATA INTEGRATION AND NETWORK ANALYSIS Data integration is crucial to recognizing signaling pathways and nodes of activity that mediate the interactions between virus and host.  ... 
doi:10.1016/b978-0-12-800964-2.00012-4 fatcat:f37t7ylusvbw7eps7mefn52x3m

Systematic Approaches towards the Development of Host-Directed Antiviral Therapeutics

Andrew Prussia, Pahk Thepchatri, James P. Snyder, Richard Plemper
2011 International Journal of Molecular Sciences  
This approach is propelled by bioinformatics analysis of genome-wide screens that greatly enhance insights into the complex network of host-pathogen interactions and generate a shortlist of potential gene  ...  targets from a multitude of candidates, thus setting the stage for a new era of rational identification of drug targets for host-directed antiviral therapies.  ...  Acknowledgments This work was supported, in part, by the Emory Institute for Drug Discovery (EIDD) (A.P., P.T., J.P.S.) and Public Health Service Grants AI071002 and AI085328 (to R.K.P.) from the NIH/NIAID  ... 
doi:10.3390/ijms12064027 pmid:21747723 pmcid:PMC3131607 fatcat:h3pdop2gdrb6rgdm4ztn3lsoc4

Influenza virus–host interactomes as a basis for antiviral drug development

Tokiko Watanabe, Yoshihiro Kawaoka
2015 Current Opinion in Virology  
development of new antiviral 33 drugs with a low propensity for the development of resistance. 34 35 36 37  ...  22 Currently, antiviral drugs that target specific viral protein functions are available for 23 the treatment of influenza; however, concern regarding the emergence of drug-24 resistant viruses is warranted  ...  Cell 2009, 442 139:1255-1267. 443  This study utilized a combination of transcriptional profiling, a yeast-two hybrid 444 screen, and an RNAi-based screen to identify host factors involved in 445 influenza  ... 
doi:10.1016/j.coviro.2015.08.008 pmid:26364134 pmcid:PMC5380926 fatcat:2bu4ako7qzdmzicoym5tf7ahde

Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation

Simon Dirmeier, Christopher Dächert, Martijn van Hemert, Ali Tas, Natacha S. Ogando, Frank van Kuppeveld, Ralf Bartenschlager, Lars Kaderali, Marco Binder, Niko Beerenwinkel, Natalia L. Komarova
2020 PLoS Computational Biology  
Subsequently the inferred estimates are spread across a network of functional interactions thereby allowing for the analysis of missing genes in the biological studies, smoothing the effect sizes of previously  ...  Genetic perturbation screens using RNA interference (RNAi) have been conducted successfully to identify host factors that are essential for the life cycle of bacteria or viruses.  ...  Acknowledgments We thank Eric Snijder and Clara Posthuma for discussions and feedback regarding the siRNA screens.  ... 
doi:10.1371/journal.pcbi.1007587 pmid:32040506 fatcat:vqtshu4yardnfobvualqryiyni

Cell-based genomic screening: elucidating virus–host interactions

Debasis Panda, Sara Cherry
2012 Current Opinion in Virology  
The recent advent of cell-based screening coupled with RNAi technology, has greatly facilitated studies focused on characterizing the virus-host interface and has expanded our understanding of cellular  ...  Characterization of these processes has revealed insights both into fundamental cellular processes as well as the nuances of viral replication.  ...  S.C. is a recipient of the Burroughs Wellcome Investigators in the Pathogenesis of Infectious Disease Award.  ... 
doi:10.1016/j.coviro.2012.10.007 pmid:23122855 pmcid:PMC3512112 fatcat:ezepktubzbhthfouuxlgakwhl4

GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data

Marie E Fahey, Melanie J Bennett, Cathal Mahon, Stefanie Jäger, Lars Pache, Dhiraj Kumar, Alex Shapiro, Kanury Rao, Sumit K Chanda, Charles S Craik, Alan D Frankel, Nevan J Krogan
2011 BMC Bioinformatics  
Results: We have developed a web-based platform, termed GPS-Prot http://www.gpsprot.org, that allows for facile integration of different HIV interaction data types as well as inclusion of interactions  ...  The increasing availability of HIV-host interaction datasets, including both physical and genetic interactions, has created a need for software tools to integrate and visualize the data.  ...  We thank Paul De Jesus for advice and excellent technical assistance with RNAi-based assays and Mike Shales for assistance with figure preparation.  ... 
doi:10.1186/1471-2105-12-298 pmid:21777475 pmcid:PMC3213248 fatcat:cx2my7mg2jgcpiidepzj7u4a2y

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response

Robin van der Lee, Qian Feng, Martijn A. Langereis, Rob ter Horst, Radek Szklarczyk, Mihai G. Netea, Arno C. Andeweg, Frank J. M. van Kuppeveld, Martijn A. Huynen, Bjoern Peters
2015 PLoS Computational Biology  
Using a Bayesian approach to integrate these signatures, we propose likely novel RLR regulators.  ...  form a tightly connected interaction network.  ...  Calculated viral miRNA targeting scores and contributed to the integration approach: RtH. Calculated RLR co-expression and contributed to the integration approach: RS.  ... 
doi:10.1371/journal.pcbi.1004553 pmid:26485378 pmcid:PMC4618338 fatcat:fojwqwnzwjhkhpeik75ibqczpi

The use of RNAi-based screens to identify host proteins involved in viral replication

Alec J Hirsch
2010 Future Microbiology  
This review summarizes the methods used in RNAi-based screening for host factors involved in virus replication, and discusses published examples of such screens.  ...  The recent development of RNAi-based techniques for protein knockdown in mammalian cells has allowed for unprecedented flexibility in the study of protein function.  ...  Acknowledgments The author thanks Jessica Smith and David Stein for helpful discussions and critical reading of this manuscript. Bibliography Papers of special note have been highlighted as:  ... 
doi:10.2217/fmb.09.121 pmid:20143951 pmcid:PMC2864646 fatcat:pk3j4enigbcrhdnkhw3u7xt6ka
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