A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments
Phage Display is a powerful method for the identification of peptide binding to targets of variable complexities and tissues, from unique molecules to the internal surfaces of vessels of living organisms. Particularly for in vivo screenings, the resulting repertoires can be very complex and difficul...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-09-01
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| Series: | Frontiers in Physiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fphys.2019.01160/full |
| _version_ | 1818941001828401152 |
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| author | Antonios Vekris Eleftherios Pilalis Eleftherios Pilalis Aristotelis Chatziioannou Aristotelis Chatziioannou Klaus G. Petry |
| author_facet | Antonios Vekris Eleftherios Pilalis Eleftherios Pilalis Aristotelis Chatziioannou Aristotelis Chatziioannou Klaus G. Petry |
| author_sort | Antonios Vekris |
| collection | DOAJ |
| description | Phage Display is a powerful method for the identification of peptide binding to targets of variable complexities and tissues, from unique molecules to the internal surfaces of vessels of living organisms. Particularly for in vivo screenings, the resulting repertoires can be very complex and difficult to study with traditional approaches. Next Generation Sequencing (NGS) opened the possibility to acquire high resolution overviews of such repertoires and thus facilitates the identification of binders of interest. Additionally, the ever-increasing amount of available genome/proteome information became satisfactory regarding the identification of putative mimicked proteins, due to the large scale on which partial sequence homology is assessed. However, the subsequent production of massive data stresses the need for high-performance computational approaches in order to perform standardized and insightful molecular network analysis. Systems-level analysis is essential for efficient resolution of the underlying molecular complexity and the extraction of actionable interpretation, in terms of systemic biological processes and pathways that are systematically perturbed. In this work we introduce PepSimili, an integrated workflow tool, which performs mapping of massive peptide repertoires on whole proteomes and delivers a streamlined, systems-level biological interpretation. The tool employs modules for modeling and filtering of background noise due to random mappings and amplifies the biologically meaningful signal through coupling with BioInfoMiner, a systems interpretation tool that employs graph-theoretic methods for prioritization of systemic processes and corresponding driver genes. The current implementation exploits the Galaxy environment and is available online. A case study using public data is presented, with and without a control selection. |
| first_indexed | 2024-12-20T06:48:36Z |
| format | Article |
| id | doaj.art-a73ebf520ed149b78d5b4d5d8ab58be3 |
| institution | Directory Open Access Journal |
| issn | 1664-042X |
| language | English |
| last_indexed | 2024-12-20T06:48:36Z |
| publishDate | 2019-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Physiology |
| spelling | doaj.art-a73ebf520ed149b78d5b4d5d8ab58be32022-12-21T19:49:37ZengFrontiers Media S.A.Frontiers in Physiology1664-042X2019-09-011010.3389/fphys.2019.01160434562A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display ExperimentsAntonios Vekris0Eleftherios Pilalis1Eleftherios Pilalis2Aristotelis Chatziioannou3Aristotelis Chatziioannou4Klaus G. Petry5UMR 1049 and U1029, INSERM, Bordeaux, FranceMetabolic Engineering and Bioinformatics Program, Institute of Chemical Biology, National Hellenic Research Foundation, Athens, GreeceeNIOS Applications P.C., Athens, GreeceMetabolic Engineering and Bioinformatics Program, Institute of Chemical Biology, National Hellenic Research Foundation, Athens, GreeceeNIOS Applications P.C., Athens, GreeceUMR 1049 and U1029, INSERM, Bordeaux, FrancePhage Display is a powerful method for the identification of peptide binding to targets of variable complexities and tissues, from unique molecules to the internal surfaces of vessels of living organisms. Particularly for in vivo screenings, the resulting repertoires can be very complex and difficult to study with traditional approaches. Next Generation Sequencing (NGS) opened the possibility to acquire high resolution overviews of such repertoires and thus facilitates the identification of binders of interest. Additionally, the ever-increasing amount of available genome/proteome information became satisfactory regarding the identification of putative mimicked proteins, due to the large scale on which partial sequence homology is assessed. However, the subsequent production of massive data stresses the need for high-performance computational approaches in order to perform standardized and insightful molecular network analysis. Systems-level analysis is essential for efficient resolution of the underlying molecular complexity and the extraction of actionable interpretation, in terms of systemic biological processes and pathways that are systematically perturbed. In this work we introduce PepSimili, an integrated workflow tool, which performs mapping of massive peptide repertoires on whole proteomes and delivers a streamlined, systems-level biological interpretation. The tool employs modules for modeling and filtering of background noise due to random mappings and amplifies the biologically meaningful signal through coupling with BioInfoMiner, a systems interpretation tool that employs graph-theoretic methods for prioritization of systemic processes and corresponding driver genes. The current implementation exploits the Galaxy environment and is available online. A case study using public data is presented, with and without a control selection.https://www.frontiersin.org/article/10.3389/fphys.2019.01160/fullphage displayGalaxy platformenrichment analysisnetwork analysisbiological interpretationReactome |
| spellingShingle | Antonios Vekris Eleftherios Pilalis Eleftherios Pilalis Aristotelis Chatziioannou Aristotelis Chatziioannou Klaus G. Petry A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments Frontiers in Physiology phage display Galaxy platform enrichment analysis network analysis biological interpretation Reactome |
| title | A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments |
| title_full | A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments |
| title_fullStr | A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments |
| title_full_unstemmed | A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments |
| title_short | A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments |
| title_sort | computational pipeline for the extraction of actionable biological information from ngs phage display experiments |
| topic | phage display Galaxy platform enrichment analysis network analysis biological interpretation Reactome |
| url | https://www.frontiersin.org/article/10.3389/fphys.2019.01160/full |
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