DRomics, a workflow to exploit dose-response omics data in ecotoxicology
Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, d...
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2023-09-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.325/ |
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| author | Delignette-Muller, Marie Laure Siberchicot, Aurélie Larras, Floriane Billoir, Elise |
| author_facet | Delignette-Muller, Marie Laure Siberchicot, Aurélie Larras, Floriane Billoir, Elise |
| author_sort | Delignette-Muller, Marie Laure |
| collection | DOAJ |
| description | Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications.
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| format | Article |
| id | doaj-art-eaec5cc3fabc4aeba7eb9740398f74c2 |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2023-09-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj-art-eaec5cc3fabc4aeba7eb9740398f74c22025-02-07T10:16:48ZengPeer Community InPeer Community Journal2804-38712023-09-01310.24072/pcjournal.32510.24072/pcjournal.325DRomics, a workflow to exploit dose-response omics data in ecotoxicology Delignette-Muller, Marie Laure0https://orcid.org/0000-0001-5453-3994Siberchicot, Aurélie1https://orcid.org/0000-0002-7638-8318Larras, Floriane2https://orcid.org/0000-0002-8345-8716Billoir, Elise3https://orcid.org/0000-0001-9012-3298Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, FranceUniversité de Lyon, Université Lyon 1, CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, FranceUniversité de Lyon, Université Lyon 1, CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, FranceUniversité de Lorraine, CNRS, LIEC, F-57000 Metz, FranceOmics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications. https://peercommunityjournal.org/articles/10.24072/pcjournal.325/Dose-response modelingBenchMark Dose (BMD)Adverse Outcome Pathway (AOP)Mode of Action (MoA)environmental risk assessmenttranscriptomicsproteomicsmetabolomicsmultiomics |
| spellingShingle | Delignette-Muller, Marie Laure Siberchicot, Aurélie Larras, Floriane Billoir, Elise DRomics, a workflow to exploit dose-response omics data in ecotoxicology Peer Community Journal Dose-response modeling BenchMark Dose (BMD) Adverse Outcome Pathway (AOP) Mode of Action (MoA) environmental risk assessment transcriptomics proteomics metabolomics multiomics |
| title | DRomics, a workflow to exploit dose-response omics data in ecotoxicology
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| title_full | DRomics, a workflow to exploit dose-response omics data in ecotoxicology
|
| title_fullStr | DRomics, a workflow to exploit dose-response omics data in ecotoxicology
|
| title_full_unstemmed | DRomics, a workflow to exploit dose-response omics data in ecotoxicology
|
| title_short | DRomics, a workflow to exploit dose-response omics data in ecotoxicology
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| title_sort | dromics a workflow to exploit dose response omics data in ecotoxicology |
| topic | Dose-response modeling BenchMark Dose (BMD) Adverse Outcome Pathway (AOP) Mode of Action (MoA) environmental risk assessment transcriptomics proteomics metabolomics multiomics |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.325/ |
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