A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings
<p dir="ltr">Transcriptome profiling data, generated via RNA sequencing, are commonly deposited in public repositories. However, these data may not be easily accessible or usable by many researchers. To enhance data reuse, we present well-annotated, partially analyzed data via a user...
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2024
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| _version_ | 1864513543739539456 |
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| author | Darawan Rinchai (742366) |
| author2 | Tobias Brummaier (9194310) Alexandra A Marr (21767573) Tanwir Habib (47644) Mohammed Toufiq (7251596) Tomoshigue Kino (21767576) François Nosten (17237) Souhaila Al Khodor (89983) Annalisa Terranegra (3486953) Rose McGready (17231) Basirudeen Syed Ahamed Kabeer (9676280) Damien Chaussabel (26369) |
| author2_role | author author author author author author author author author author author |
| author_facet | Darawan Rinchai (742366) Tobias Brummaier (9194310) Alexandra A Marr (21767573) Tanwir Habib (47644) Mohammed Toufiq (7251596) Tomoshigue Kino (21767576) François Nosten (17237) Souhaila Al Khodor (89983) Annalisa Terranegra (3486953) Rose McGready (17231) Basirudeen Syed Ahamed Kabeer (9676280) Damien Chaussabel (26369) |
| author_role | author |
| dc.creator.none.fl_str_mv | Darawan Rinchai (742366) Tobias Brummaier (9194310) Alexandra A Marr (21767573) Tanwir Habib (47644) Mohammed Toufiq (7251596) Tomoshigue Kino (21767576) François Nosten (17237) Souhaila Al Khodor (89983) Annalisa Terranegra (3486953) Rose McGready (17231) Basirudeen Syed Ahamed Kabeer (9676280) Damien Chaussabel (26369) |
| dc.date.none.fl_str_mv | 2024-04-02T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1093/database/baae021 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/A_data_browsing_application_for_accessing_gene_and_module-level_blood_transcriptome_profiles_of_healthy_pregnant_women_from_high-_and_low-resource_settings/29624975 |
| 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 Reproductive medicine RNA sequencing Transcriptome profiling Blood transcriptomics Pregnancy Gene expression Data visualization Bioinformatics tool Maternal health |
| dc.title.none.fl_str_mv | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">Transcriptome profiling data, generated via RNA sequencing, are commonly deposited in public repositories. However, these data may not be easily accessible or usable by many researchers. To enhance data reuse, we present well-annotated, partially analyzed data via a user-friendly web application. This project involved transcriptome profiling of blood samples from 15 healthy pregnant women in a low-resource setting, taken at 6 consecutive time points beginning from the first trimester. Additional blood transcriptome profiles were retrieved from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) public repository, representing a cohort of healthy pregnant women from a high-resource setting. We analyzed these datasets using the fixed BloodGen3 module repertoire. We deployed a web application, accessible at https://thejacksonlaboratory.shinyapps.io/BloodGen3_Pregnancy/which displays the module-level analysis results from both original and public pregnancy blood transcriptome datasets. Users can create custom fingerprint grid and heatmap representations via various navigation options, useful for reports and manuscript preparation. The web application serves as a standalone resource for exploring blood transcript abundance changes during pregnancy. Alternatively, users can integrate it with similar applications developed for earlier publications to analyze transcript abundance changes of a given BloodGen3 signature across a range of disease cohorts.</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/baae021" target="_blank">https://dx.doi.org/10.1093/database/baae021</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_4a697ee87afa8084e3430ff6bfe7f99c |
| identifier_str_mv | 10.1093/database/baae021 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/29624975 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settingsDarawan Rinchai (742366)Tobias Brummaier (9194310)Alexandra A Marr (21767573)Tanwir Habib (47644)Mohammed Toufiq (7251596)Tomoshigue Kino (21767576)François Nosten (17237)Souhaila Al Khodor (89983)Annalisa Terranegra (3486953)Rose McGready (17231)Basirudeen Syed Ahamed Kabeer (9676280)Damien Chaussabel (26369)Biological sciencesGeneticsBiomedical and clinical sciencesImmunologyReproductive medicineRNA sequencingTranscriptome profilingBlood transcriptomicsPregnancyGene expressionData visualizationBioinformatics toolMaternal health<p dir="ltr">Transcriptome profiling data, generated via RNA sequencing, are commonly deposited in public repositories. However, these data may not be easily accessible or usable by many researchers. To enhance data reuse, we present well-annotated, partially analyzed data via a user-friendly web application. This project involved transcriptome profiling of blood samples from 15 healthy pregnant women in a low-resource setting, taken at 6 consecutive time points beginning from the first trimester. Additional blood transcriptome profiles were retrieved from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) public repository, representing a cohort of healthy pregnant women from a high-resource setting. We analyzed these datasets using the fixed BloodGen3 module repertoire. We deployed a web application, accessible at https://thejacksonlaboratory.shinyapps.io/BloodGen3_Pregnancy/which displays the module-level analysis results from both original and public pregnancy blood transcriptome datasets. Users can create custom fingerprint grid and heatmap representations via various navigation options, useful for reports and manuscript preparation. The web application serves as a standalone resource for exploring blood transcript abundance changes during pregnancy. Alternatively, users can integrate it with similar applications developed for earlier publications to analyze transcript abundance changes of a given BloodGen3 signature across a range of disease cohorts.</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/baae021" target="_blank">https://dx.doi.org/10.1093/database/baae021</a></p>2024-04-02T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1093/database/baae021https://figshare.com/articles/journal_contribution/A_data_browsing_application_for_accessing_gene_and_module-level_blood_transcriptome_profiles_of_healthy_pregnant_women_from_high-_and_low-resource_settings/29624975CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/296249752024-04-02T03:00:00Z |
| spellingShingle | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings Darawan Rinchai (742366) Biological sciences Genetics Biomedical and clinical sciences Immunology Reproductive medicine RNA sequencing Transcriptome profiling Blood transcriptomics Pregnancy Gene expression Data visualization Bioinformatics tool Maternal health |
| status_str | publishedVersion |
| title | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings |
| title_full | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings |
| title_fullStr | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings |
| title_full_unstemmed | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings |
| title_short | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings |
| title_sort | A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings |
| topic | Biological sciences Genetics Biomedical and clinical sciences Immunology Reproductive medicine RNA sequencing Transcriptome profiling Blood transcriptomics Pregnancy Gene expression Data visualization Bioinformatics tool Maternal health |