A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases
<p dir="ltr">Prevalence of allergies has reached ~20% of population in developed countries and sensitization rate to one or more allergens among school age children are approaching 50%. However, the combination of the complexity of atopic allergy susceptibility/development and enviro...
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2019
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| author | Susie S Y Huang (18805921) |
| author2 | Fatima Al Ali (13210926) Sabri Boughorbel (846228) Mohammed Toufiq (7251596) Damien Chaussabel (26369) Mathieu Garand (4861942) |
| author2_role | author author author author author |
| author_facet | Susie S Y Huang (18805921) Fatima Al Ali (13210926) Sabri Boughorbel (846228) Mohammed Toufiq (7251596) Damien Chaussabel (26369) Mathieu Garand (4861942) |
| author_role | author |
| dc.creator.none.fl_str_mv | Susie S Y Huang (18805921) Fatima Al Ali (13210926) Sabri Boughorbel (846228) Mohammed Toufiq (7251596) Damien Chaussabel (26369) Mathieu Garand (4861942) |
| dc.date.none.fl_str_mv | 2019-07-10T06:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1093/database/baz066 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/A_curated_collection_of_transcriptome_datasets_to_investigate_the_molecular_mechanisms_of_immunoglobulin_E-mediated_atopic_diseases/26015824 |
| 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 Allergic disease Sensitization rates Atopic diseases Allergic rhinitis Asthma Atopic dermatitis Immune response Gene biomarkers Genetic susceptibility |
| dc.title.none.fl_str_mv | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">Prevalence of allergies has reached ~20% of population in developed countries and sensitization rate to one or more allergens among school age children are approaching 50%. However, the combination of the complexity of atopic allergy susceptibility/development and environmental factors has made identification of gene biomarkers challenging. The amount of publicly accessible transcriptomic data presents an unprecedented opportunity for mechanistic discoveries and validation of complex disease signatures across studies. However, this necessitates structured methodologies and visual tools for the interpretation of results. Here, we present a curated collection of transcriptomic datasets relevant to immunoglobin E-mediated atopic diseases (ranging from allergies to primary immunodeficiencies). Thirty-three datasets from the Gene Expression Omnibus, encompassing 1860 transcriptome profiles, were made available on the Gene Expression Browser (GXB), an online and open-source web application that allows for the query, visualization and annotation of metadata. The thematic compositions, disease categories, sample number and platforms of the collection are described. Ranked gene lists and sample grouping are used to facilitate data visualization/interpretation and are available online via GXB (<a href="http://ige.gxbsidra.org/dm3/geneBrowser/list" rel="noreferrer" target="_blank">http://ige.gxbsidra.org/dm3/geneBrowser/list</a>). Dataset validation using associated publications showed good concordance in GXB gene expression trend and fold-change.</p><h2>Other Information</h2><p dir="ltr">Published in: Database<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1093/database/baz066" target="_blank">https://dx.doi.org/10.1093/database/baz066</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_ad319715e84dfb797b36d582d1e2d348 |
| identifier_str_mv | 10.1093/database/baz066 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26015824 |
| publishDate | 2019 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseasesSusie S Y Huang (18805921)Fatima Al Ali (13210926)Sabri Boughorbel (846228)Mohammed Toufiq (7251596)Damien Chaussabel (26369)Mathieu Garand (4861942)Biological sciencesGeneticsBiomedical and clinical sciencesImmunologyAllergic diseaseSensitization ratesAtopic diseasesAllergic rhinitisAsthmaAtopic dermatitisImmune responseGene biomarkersGenetic susceptibility<p dir="ltr">Prevalence of allergies has reached ~20% of population in developed countries and sensitization rate to one or more allergens among school age children are approaching 50%. However, the combination of the complexity of atopic allergy susceptibility/development and environmental factors has made identification of gene biomarkers challenging. The amount of publicly accessible transcriptomic data presents an unprecedented opportunity for mechanistic discoveries and validation of complex disease signatures across studies. However, this necessitates structured methodologies and visual tools for the interpretation of results. Here, we present a curated collection of transcriptomic datasets relevant to immunoglobin E-mediated atopic diseases (ranging from allergies to primary immunodeficiencies). Thirty-three datasets from the Gene Expression Omnibus, encompassing 1860 transcriptome profiles, were made available on the Gene Expression Browser (GXB), an online and open-source web application that allows for the query, visualization and annotation of metadata. The thematic compositions, disease categories, sample number and platforms of the collection are described. Ranked gene lists and sample grouping are used to facilitate data visualization/interpretation and are available online via GXB (<a href="http://ige.gxbsidra.org/dm3/geneBrowser/list" rel="noreferrer" target="_blank">http://ige.gxbsidra.org/dm3/geneBrowser/list</a>). Dataset validation using associated publications showed good concordance in GXB gene expression trend and fold-change.</p><h2>Other Information</h2><p dir="ltr">Published in: Database<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1093/database/baz066" target="_blank">https://dx.doi.org/10.1093/database/baz066</a></p>2019-07-10T06:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1093/database/baz066https://figshare.com/articles/journal_contribution/A_curated_collection_of_transcriptome_datasets_to_investigate_the_molecular_mechanisms_of_immunoglobulin_E-mediated_atopic_diseases/26015824CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/260158242019-07-10T06:00:00Z |
| spellingShingle | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases Susie S Y Huang (18805921) Biological sciences Genetics Biomedical and clinical sciences Immunology Allergic disease Sensitization rates Atopic diseases Allergic rhinitis Asthma Atopic dermatitis Immune response Gene biomarkers Genetic susceptibility |
| status_str | publishedVersion |
| title | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases |
| title_full | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases |
| title_fullStr | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases |
| title_full_unstemmed | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases |
| title_short | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases |
| title_sort | A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases |
| topic | Biological sciences Genetics Biomedical and clinical sciences Immunology Allergic disease Sensitization rates Atopic diseases Allergic rhinitis Asthma Atopic dermatitis Immune response Gene biomarkers Genetic susceptibility |