A comprehensive database for integrated analysis of omics data in autoimmune diseases

BMC Bioinformatics, vol. 22, pp. 343

Abstract

BACKGROUND: Autoimmune diseases are heterogeneous pathologies with difficult diagnosis and few therapeutic options. In the last decade, several omics studies have provided significant insights into the molecular mechanisms of these diseases. Nevertheless, data from different cohorts and pathologies are stored independently in public repositories and a unified resource is imperative to assist researchers in this field. RESULTS: Here, we present Autoimmune Diseases Explorer ( https://adex.genyo.es ), a database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases. The database provides, in an easy-to-use environment, advanced data analysis and statistical methods for exploring omics datasets, including meta-analysis, differential expression or pathway analysis. CONCLUSIONS: This is the first omics database focused on autoimmune diseases. This resource incorporates homogeneously processed data to facilitate integrative analyses among studies.

Authors 16

1. Jordi Martorell‐Marugán

   Universidad de Granada · Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

   Affiliation as printed

   Atrys Health S.A., Barcelona, Spain

   Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain

2. Raúl López-Domínguez

   Universidad de Granada · Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

   Affiliation as printed

   Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain

3. Adrián García-Moreno

   Universidad de Granada · Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

   Affiliation as printed

   Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain

4. Daniel Toro Dominguez

   Universidad de Granada · Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

   Affiliation as printed

   Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain

   Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain

5. Juan Antonio Villatoro-García

   Universidad de Granada · Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

   Affiliation as printed

   Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain

   Department of Statistics, University of Granada, 18071, Granada, Spain

6. Guillermo Barturen

   Universidad de Granada · Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

   Affiliation as printed

   Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain

7. Adoración Martín-Gómez

   Hospital de Poniente

   Affiliation as printed

   Nephrology Units, AADEA: Asociación Andaluza de Enfermedades Autoinmunes, Hospital de Poniente, 04700, Almería, Spain

8. Kevin Troulé

   Spanish National Cancer Research Centre

   Affiliation as printed

   Bioinformatics Unit, Spanish National Cancer Center, CNIO, Madrid, Spain

9. Gonzalo Goméz-López

   Spanish National Cancer Research Centre

   Affiliation as printed

   Bioinformatics Unit, Spanish National Cancer Center, CNIO, Madrid, Spain

10. Fátima Al‐Shahrour

    Spanish National Cancer Research Centre

    Affiliation as printed

    Bioinformatics Unit, Spanish National Cancer Center, CNIO, Madrid, Spain

11. Víctor González‐Rumayor
    Affiliation as printed

    Atrys Health S.A., Barcelona, Spain

12. María Peña-Chilet

    Fundación Progreso y Salud · Centre for Biomedical Network Research on Rare Diseases · Instituto de Biomedicina de Sevilla

    Affiliation as printed

    Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013, Seville, Spain

    Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocío, 41013, Seville, Spain

    Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Seville, Spain

13. Joaquı́n Dopazo

    Fundación Progreso y Salud · Centre for Biomedical Network Research on Rare Diseases · Instituto de Biomedicina de Sevilla · Hospital Universitario Virgen del Rocío

    Affiliation as printed

    Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013, Seville, Spain

    Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocío, 41013, Seville, Spain

    Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Seville, Spain

    INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, 42013, Seville, Spain

14. Julio Sáez-Rodríguez Aachen Joint Research Centre for Computational Biomedicine (JRC-COMBINE) Faculty of Medicine

    European Bioinformatics Institute · Heidelberg University · University Hospital Heidelberg · RWTH Aachen University

    Affiliation as printed

    European Molecular Biology Laboratory-The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK

    Institute for Computational Biomedicine, Bioquant Heidelberg, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, 69120, Heidelberg, Germany

    Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074, Aachen, Germany

15. Marta Eugenia Alarcón-Riquelme

    Universidad de Granada · Karolinska Institutet · Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

    Affiliation as printed

    Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain

    Unit of Chronic Inflammatory Diseases, Institute of Environmental Medicine, Karolinska Institutet, 17177, Stockholm, Sweden

16. Pedro Carmona‐Sáez corresponding

    Universidad de Granada · Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

    Affiliation as printed

    Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain. pedro.carmona@genyo.es

    Department of Statistics, University of Granada, 18071, Granada, Spain. pedro.carmona@genyo.es

    Department of Statistics, University of Granada, 18071, Granada, Spain