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  • Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development

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Chest clinic
Research and guideline updates
Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development
  1. Yina Du1,
  2. Joseph A Kitzmiller1,
  3. Anusha Sridharan1,
  4. Anne K Perl1,
  5. James P Bridges1,
  6. Ravi S Misra4,
  7. Gloria S Pryhuber4,
  8. Thomas J Mariani4,
  9. Soumyaroop Bhattacharya4,
  10. Minzhe Guo1,
  11. S Steven Potter2,
  12. Phillip Dexheimer3,
  13. Bruce Aronow3,
  14. Alan H Jobe1,
  15. Jeffrey A Whitsett1,
  16. Yan Xu1,3
  1. 1The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
  2. 2Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
  3. 3Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
  4. 4Department of Pediatrics, University of Rochester, Rochester, New York, USA
  1. Correspondence to Dr Yan Xu, The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Yan.Xu{at}cchmc.org

Abstract

‘LungGENS’, our previously developed web tool for mapping single-cell gene expression in the developing lung, has been well received by the pulmonary research community. With continued support from the ‘LungMAP’ consortium, we extended the scope of the LungGENS database to accommodate transcriptomics data from pulmonary tissues and cells from human and mouse at different stages of lung development. Lung Gene Expression Analysis (LGEA) web portal is an extended version of LungGENS useful for the analysis, display and interpretation of gene expression patterns obtained from single cells, sorted cell populations and whole lung tissues. The LGEA web portal is freely available at http://research.cchmc.org/pbge/lunggens/mainportal.html.

  • Airway Epithelium
  • Surfactant protein
  • Systemic disease and lungs
  • TTF-1

This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/

https://doi.org/10.1136/thoraxjnl-2016-209598

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    Footnotes

    • Twitter Follow Yan Xu @YanXu_Cincy

    • Contributors YX and YD conceived and designed the web application. YD developed the database and web application. JAK, AS, AKP, JPB and JAW designed and conducted mouse single-cell and sorted cell RNA-seq experiments. AHJ and JAW designed and conducted rhesus macaque RNA-seq experiments. RSM, GSP, TJM and SB designed and conducted human sorted cell RNA-seq experiments. SSP, JAW, PD and BA conceived and performed the single-cell experiments, helped generate and interpret the lung single-cell data. MG, YD and YX contributed to data analysis and interpretation. YD, JAW and YX contributed to the writing of the manuscript. All authors have read and provided inputs to the manuscript.

    • Funding NHLBI U01 HL122642 (LungMAP).

    • Competing interests None declared.

    • Provenance and peer review Not commissioned; externally peer reviewed.

    • Data sharing statement LGEA web portal and LungGENS are freely available for non-commercial use at http://research.cchmc.org/pbge/lunggens/mainportal.html and data will be integrated with other omics data and lung image data at ‘BREATH’ database and display on the LungMAP website (http://www.lungmap.net/).