Thorax. 2017 May;72(5):481-484.

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

 

Yina Du1, Joseph A Kitzmiller1, Anusha Sridharan1, Anne K Perl1, James P Bridges1, Ravi S Misra4, Gloria S Pryhuber4, Thomas J Mariani4, Soumyaroop. Bhattacharya4, Minzhe Guo1, S. Steven Potter2, Phillip Dexheimer3, Bruce Aronow3, Alan H. Jobe1, Charles Ansong5, Jeffrey A Whitsett1 and Yan Xu1,3

Affiliations 

1The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, 2Division of Developmental Biology, 3Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA. 4Department of Pediatrics, University of Rochester, Rochester, NY, USA. 5Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA.

 

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.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520249/

 

Supplement

LGEA web portal offers user-friendly and comprehensive web-based query functions on extensive genomic/image data sets from human and mouse at different stages of lung development. In addition to the transcriptional mapping of normal lung development studies, the current data begin to map abnormal lung tissues and cells. With continued support from the ‘LungMAP’ consortium, we extended the scope of the LGEA database to include other omics data such as proteomics and epigenetic data from lung developmental studies. This supplemental file will introduce the new functionalities and features of LGEA web portal.

“LungDisease” panel was added into LGEA web portal for users to search altered gene expression patterns, disease related signatures and lung disease related images (Figure 1). Currently available data sets include single-cell and sorted cell RNA sequencing of epithelial cells isolated from the peripheral regions of the normal and IPF lung [1] and single-cell RNA-seq of NKX2-1–expressing human lung progenitors derived from patient-specific cystic fibrosis pluripotent stem cells (iPSCs) [2]. “LungDisease” panel takes gene symbol and pre-defined cell type as query inputs, LGEA retrieves data from the “LungDisease” database to provide cell-specific gene expression patterns for each predicted cell type and associated gene signatures for cell types of interest. In addition to the visualization tools associated with the previous version of LGEA web-portal (i.e., expression heatmap, mean expression bar graph, statistical summary of each gene at each given cell type) [3], we introduced a three-dimension interactive scatter plot for principal component analysis, Figure 2A. Users can choose color by cell types, by patient ID, by diagnosis or by gene expression. These color setting functions provide users an interactive way to explore gene of interest in IPF study. Another new feature is that the queried gene expression can be overlaid on a 3D scatter plot using gradient color scale. Figure 2A shows an example of query by gene using Surfactant protein C (SFTPC) as input. SFTPC is highly enriched in normal AT2 cells compared to other IPF cells (Figure 2A-2B).  Hyperlinks of lung images by disease types are provided to redirect the web interface to the Lung Image web collection (https://research.cchmc.org/lungimage/) hosted by Dr Whitsett’s laboratory. Current available lung disease images include images from BronchoPulmonary Dysplasia (BPD), Primary Alveolar Capillary Dysplasia (C16-00104), Lung Growth Disorder (MC17-1H and MC17-3H).

“LungEpigenetic” panel is added using ChIP-seq data during mouse lung development downloaded from ENCODE (https://www.encodeproject.org/)[4]. “LungEpigenetic” query displays queried gene using UCSC Genome Browser with selected tracks enabled. Users can choose developmental stages and/or specific histone modifications to retrieve results displayed on UCSC Genome Browser (Figure 3).

“LungProteomics” provides protein centered query functions. Proteomic data are generated at Pacific Northwest National Laboratory (PNNL) led by Dr. Charles Ansong. Output includes the average expression of protein and corresponding mRNA, the correlation of protein and mRNA expression profiles, and an overview of the levels of expression of the queried protein/gene expression across all data sets in the LGEA database using a monocolor heatmap. Sample screenshots of “LungProteomics” query results are shown in Figure 4.

“LGEA toolbox” panel was created to facilitate users to perform further comparisons and integration analyses of LGEA data. Current toolbox includes “Gene at glance”, “SigComparison”, “LDProfiles” and other internal and external resources. We will continue updating the database and developing new query functions of the LGEA web portal as new datasets are added. The LGEA web portal home page will provide updates of newest data, tool releases and associated publications in the news panel (https://research.cchmc.org/pbge/lunggens/mainportal.html). These data also will be available at the Breath, LungMAP website.

 

 

Figure 1: LGEA web portal home page. Recently developed web panels were highlighted in red box.

 

 

Figure 2: Sample screenshots of “LungDisease” panel in LGEA web portal: 3D interactive scatter plot and gene expression comparison across cell types.

 

 

Figure 3: Sample screenshots of query result of “LungEpigenetics” panel in LGEA web portal.

 

 

Figure 4: Sample screenshots of query result of “LungProteomics” panel in LGEA web portal.

 

References:

  1. Xu Y, Mizuno T, Sridharan A, et al. Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis. JCI Insight 2016;1(20):e90558 doi: 10.1172/jci.insight.90558[published Online First: Epub Date]|.
  2. Hawkins F, Kramer P, Jacob A, et al. Prospective isolation of NKX2-1-expressing human lung progenitors derived from pluripotent stem cells. J Clin Invest 2017;127(6):2277-94 doi: 10.1172/JCI89950[published Online First: Epub Date]|.
  3. Du Y, Kitzmiller JA, Sridharan A, et al. Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development. Thorax 2017;72(5):481-84 doi: 10.1136/thoraxjnl-2016-209598[published Online First: Epub Date]|.
  4. Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489(7414):57-74 doi: 10.1038/nature11247[published Online First: Epub Date]|.