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

  title={Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development},
  author={Yina Du and Joseph A. Kitzmiller and Anusha Sridharan and Anne-Karina T. Perl and James P. Bridges and Ravi S. Misra and Gloria S. Pryhuber and Thomas J. Mariani and Soumyaroop Bhattacharya and Minzhe Guo and S. Steven Potter and Phillip J. Dexheimer and Bruce J. Aronow and Alan H. Jobe and Jeffrey A. Whitsett and Yan Xu},
  pages={481 - 484}
‘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… 
LungMAP: The Molecular Atlas of Lung Development Program
A brief description of research conducted by the consortium, database, and portal development and upcoming features that will enhance the LungMAP experience for a community of users are presented.
Integration of transcriptomic and proteomic data identifies biological functions in cell populations from human infant lung.
  • Yina Du, G. Clair, Yan Xu
  • Biology
    American journal of physiology. Lung cellular and molecular physiology
  • 2019
Comparison of mRNA and protein profiles from purified endothelial, epithelial, immune, and mesenchymal cells from normal human infant lung tissue indicated an essential framework for the function of each cell type.
Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung
These ontologies standardize and expand current terminology for fetal and adult lungs, providing a qualitative framework for data annotation, retrieval, and integration across a wide variety of datasets in the BREATH database.
Lung at a Glance: an integrative web toolset of lung ontology, imaging and single cell omics
“Lung-at-a-glance” is an easy-to-use web toolset for visualizing and interoperating complex omics and imaging data, providing an interactive web interface to bridge lung anatomic ontology classifications to lung histology and immunofluorescence confocal images, and cell-type-specific gene expression.
Time-resolved proteome profiling of normal lung development.
The data support the cell proliferation that characterizes early lung development and highlight responses of the lung to exposure to a nonsterile oxygen-rich ambient environment and the important role of lipid (surfactant) metabolism in lung development.
Transcriptional characterisation of human lung cells identifies novel mesenchymal lineage markers
The data suggest that specification of distinct airway and vascular smooth muscle cell phenotypes is established early in development and can be identified using the markers provided.
OTUB1 regulates lung development, adult lung tissue homeostasis, and respiratory control
It is proposed that OTUB1 is a negative regulator of mTOR signaling with essential functions for lung cell proliferation, lung development, adult lung tissue homeostasis, and respiratory regulation.
Integrating multi-omics longitudinal data to reconstruct networks underlying lung development.
A detailed comprehensive and interactive model is developed that provides information about the major expression trajectories, the regulators of specific key events, and the impact of epigenetic changes about the regulation of innate immunity during lung development.
Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis
How transcriptomic studies led to identification of novel genes and pathways involved in the human IPF lung such as: matrix metalloproteinases, WNT pathway, epithelial genes, role of microRNAs among others, as well as conceptual insights such as the involvement of developmental pathways and deep shifts in epithelial and fibroblast phenotypes are described.


‘LungGENS’: a web-based tool for mapping single-cell gene expression in the developing lung
We developed LungGENS (Lung Gene Expression iN Single-cell), a web-based bioinformatics resource for querying single-cell gene expression databases by entering a gene symbol or a list of genes or
Expression profiling of the developing mouse lung: insights into the establishment of the extracellular matrix.
A comprehensive gene expression profiling of the entire process of murine lung development using oligonucleotide-based microarrays reveals the expression pattern of approximately 11,000 genes throughout the morphologic stages of lung development.
Transcriptional Programs Controlling Perinatal Lung Maturation
The present study systemically mapped key regulators, bioprocesses, and transcriptional networks controlling lung maturation, providing the basis for new therapeutic strategies to enhance lung function in preterm infants.
SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
This study presents a generally applicable analytic pipeline (SINCERA: a computational pipeline for SINgle CEll RNA-seq profiling Analysis) for processing scRNA-seq data from a whole organ or sorted cells and distinguished major cell types of fetal mouse lung.