An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity
<p dir="ltr">In the field of complex autoimmune diseases such as systemic lupus erythematosus (SLE), systems immunology approaches have proven invaluable in translational research settings. Large-scale datasets of transcriptome profiling have been collected and made available to the...
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| مؤلفون آخرون: | , , , , |
| منشور في: |
2024
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| _version_ | 1864513542148849664 |
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| author | Eléonore Bettacchioli (21842351) |
| author2 | Laurent Chiche (6463) Damien Chaussabel (26369) Divi Cornec (795436) Noémie Jourde-Chiche (3122955) Darawan Rinchai (742366) |
| author2_role | author author author author author |
| author_facet | Eléonore Bettacchioli (21842351) Laurent Chiche (6463) Damien Chaussabel (26369) Divi Cornec (795436) Noémie Jourde-Chiche (3122955) Darawan Rinchai (742366) |
| author_role | author |
| dc.creator.none.fl_str_mv | Eléonore Bettacchioli (21842351) Laurent Chiche (6463) Damien Chaussabel (26369) Divi Cornec (795436) Noémie Jourde-Chiche (3122955) Darawan Rinchai (742366) |
| dc.date.none.fl_str_mv | 2024-05-28T09:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1093/database/baae045 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/An_interactive_web_application_for_exploring_systemic_lupus_erythematosus_blood_transcriptomic_diversity/29715803 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Biomedical and clinical sciences Immunology Autoimmune diseases Systems immunology Transcriptomics Gene expression profiling Microarray data LUPUCE cohort |
| dc.title.none.fl_str_mv | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">In the field of complex autoimmune diseases such as systemic lupus erythematosus (SLE), systems immunology approaches have proven invaluable in translational research settings. Large-scale datasets of transcriptome profiling have been collected and made available to the research community in public repositories, but remain poorly accessible and usable by mainstream researchers. Enabling tools and technologies facilitating investigators’ interaction with large-scale datasets such as user-friendly web applications could promote data reuse and foster knowledge discovery. Microarray blood transcriptomic data from the LUPUCE cohort (publicly available on Gene Expression Omnibus, GSE49454), which comprised 157 samples from 62 adult SLE patients, were analyzed with the third-generation (BloodGen3) module repertoire framework, which comprises modules and module aggregates. These well-characterized samples corresponded to different levels of disease activity, different types of flares (including biopsy-proven lupus nephritis), different auto-antibody profiles and different levels of interferon signatures. A web application was deployed to present the aggregate-level, module-level and gene-level analysis results from LUPUCE dataset. Users can explore the similarities and heterogeneity of SLE samples, navigate through different levels of analysis, test hypotheses and generate custom fingerprint grids and heatmaps, which may be used in reports or manuscripts. This resource is available via this link: https://immunology-research.shinyapps.io/LUPUCE/. This web application can be employed as a stand-alone resource to explore changes in blood transcript profiles in SLE, and their relation to clinical and immunological parameters, to generate new research hypotheses.</p><h2>Other Information</h2><p dir="ltr">Published in: Database<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1093/database/baae045" target="_blank">https://dx.doi.org/10.1093/database/baae045</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_9f3a34a016410794b05341274acdd2a2 |
| identifier_str_mv | 10.1093/database/baae045 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/29715803 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversityEléonore Bettacchioli (21842351)Laurent Chiche (6463)Damien Chaussabel (26369)Divi Cornec (795436)Noémie Jourde-Chiche (3122955)Darawan Rinchai (742366)Biological sciencesGeneticsBiomedical and clinical sciencesImmunologyAutoimmune diseasesSystems immunologyTranscriptomicsGene expression profilingMicroarray dataLUPUCE cohort<p dir="ltr">In the field of complex autoimmune diseases such as systemic lupus erythematosus (SLE), systems immunology approaches have proven invaluable in translational research settings. Large-scale datasets of transcriptome profiling have been collected and made available to the research community in public repositories, but remain poorly accessible and usable by mainstream researchers. Enabling tools and technologies facilitating investigators’ interaction with large-scale datasets such as user-friendly web applications could promote data reuse and foster knowledge discovery. Microarray blood transcriptomic data from the LUPUCE cohort (publicly available on Gene Expression Omnibus, GSE49454), which comprised 157 samples from 62 adult SLE patients, were analyzed with the third-generation (BloodGen3) module repertoire framework, which comprises modules and module aggregates. These well-characterized samples corresponded to different levels of disease activity, different types of flares (including biopsy-proven lupus nephritis), different auto-antibody profiles and different levels of interferon signatures. A web application was deployed to present the aggregate-level, module-level and gene-level analysis results from LUPUCE dataset. Users can explore the similarities and heterogeneity of SLE samples, navigate through different levels of analysis, test hypotheses and generate custom fingerprint grids and heatmaps, which may be used in reports or manuscripts. This resource is available via this link: https://immunology-research.shinyapps.io/LUPUCE/. This web application can be employed as a stand-alone resource to explore changes in blood transcript profiles in SLE, and their relation to clinical and immunological parameters, to generate new research hypotheses.</p><h2>Other Information</h2><p dir="ltr">Published in: Database<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1093/database/baae045" target="_blank">https://dx.doi.org/10.1093/database/baae045</a></p>2024-05-28T09:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1093/database/baae045https://figshare.com/articles/journal_contribution/An_interactive_web_application_for_exploring_systemic_lupus_erythematosus_blood_transcriptomic_diversity/29715803CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/297158032024-05-28T09:00:00Z |
| spellingShingle | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity Eléonore Bettacchioli (21842351) Biological sciences Genetics Biomedical and clinical sciences Immunology Autoimmune diseases Systems immunology Transcriptomics Gene expression profiling Microarray data LUPUCE cohort |
| status_str | publishedVersion |
| title | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity |
| title_full | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity |
| title_fullStr | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity |
| title_full_unstemmed | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity |
| title_short | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity |
| title_sort | An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity |
| topic | Biological sciences Genetics Biomedical and clinical sciences Immunology Autoimmune diseases Systems immunology Transcriptomics Gene expression profiling Microarray data LUPUCE cohort |