Literature DB >> 26130332

'LungGENS': a web-based tool for mapping single-cell gene expression in the developing lung.

Yina Du1, Minzhe Guo2, Jeffrey A Whitsett1, Yan Xu3.   

Abstract

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 selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables. LungGENS will be broadly applicable in respiratory research, providing a cell-specific RNA expression resource at single-cell resolution. LungGENS is freely available for non-commercial use at https://research.cchmc.org/pbge/lunggens/default.html. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Entities:  

Keywords:  Airway Epithelium; Surfactant protein; Systemic disease and lungs; TTF-1

Mesh:

Substances:

Year:  2015        PMID: 26130332      PMCID: PMC4641439          DOI: 10.1136/thoraxjnl-2015-207035

Source DB:  PubMed          Journal:  Thorax        ISSN: 0040-6376            Impact factor:   9.139


  5 in total

1.  Expression profiling of the developing mouse lung: insights into the establishment of the extracellular matrix.

Authors:  Thomas J Mariani; Jeremy J Reed; Steven D Shapiro
Journal:  Am J Respir Cell Mol Biol       Date:  2002-05       Impact factor: 6.914

2.  A gene atlas of the mouse and human protein-encoding transcriptomes.

Authors:  Andrew I Su; Tim Wiltshire; Serge Batalov; Hilmar Lapp; Keith A Ching; David Block; Jie Zhang; Richard Soden; Mimi Hayakawa; Gabriel Kreiman; Michael P Cooke; John R Walker; John B Hogenesch
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-09       Impact factor: 11.205

3.  ToppGene Suite for gene list enrichment analysis and candidate gene prioritization.

Authors:  Jing Chen; Eric E Bardes; Bruce J Aronow; Anil G Jegga
Journal:  Nucleic Acids Res       Date:  2009-05-22       Impact factor: 16.971

4.  Transcriptional programs controlling perinatal lung maturation.

Authors:  Yan Xu; Yanhua Wang; Valérie Besnard; Machiko Ikegami; Susan E Wert; Caleb Heffner; Stephen A Murray; Leah Rae Donahue; Jeffrey A Whitsett
Journal:  PLoS One       Date:  2012-08-20       Impact factor: 3.240

5.  Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq.

Authors:  Barbara Treutlein; Doug G Brownfield; Angela R Wu; Norma F Neff; Gary L Mantalas; F Hernan Espinoza; Tushar J Desai; Mark A Krasnow; Stephen R Quake
Journal:  Nature       Date:  2014-04-13       Impact factor: 49.962

  5 in total
  65 in total

1.  Integrating multiomics longitudinal data to reconstruct networks underlying lung development.

Authors:  Jun Ding; Farida Ahangari; Celia R Espinoza; Divya Chhabra; Teodora Nicola; Xiting Yan; Charitharth V Lal; James S Hagood; Naftali Kaminski; Ziv Bar-Joseph; Namasivayam Ambalavanan
Journal:  Am J Physiol Lung Cell Mol Physiol       Date:  2019-08-21       Impact factor: 5.464

2.  Continuous-state HMMs for modeling time-series single-cell RNA-Seq data.

Authors:  Chieh Lin; Ziv Bar-Joseph
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

3.  Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development.

Authors:  Mehari Endale; Shawn Ahlfeld; Erik Bao; Xiaoting Chen; Jenna Green; Zach Bess; Matthew T Weirauch; Yan Xu; Anne Karina Perl
Journal:  Dev Biol       Date:  2017-04-11       Impact factor: 3.582

4.  Sin3a regulates epithelial progenitor cell fate during lung development.

Authors:  Changfu Yao; Gianni Carraro; Bindu Konda; Xiangrong Guan; Takako Mizuno; Norika Chiba; Matthew Kostelny; Adrianne Kurkciyan; Gregory David; Jonathan L McQualter; Barry R Stripp
Journal:  Development       Date:  2017-06-15       Impact factor: 6.868

Review 5.  Building and Regenerating the Lung Cell by Cell.

Authors:  Jeffrey A Whitsett; Tanya V Kalin; Yan Xu; Vladimir V Kalinichenko
Journal:  Physiol Rev       Date:  2019-01-01       Impact factor: 37.312

6.  Reply to D'Alessandro-Gabazza et al.: Risks of Treating Idiopathic Pulmonary Fibrosis with a TAM Receptor Kinase Inhibitor.

Authors:  Milena S Espindola; David M Habiel; Cory M Hogaboam
Journal:  Am J Respir Crit Care Med       Date:  2018-10-01       Impact factor: 21.405

7.  Role for Cela1 in Postnatal Lung Remodeling and Alpha-1 Antitrypsin-Deficient Emphysema.

Authors:  Rashika Joshi; Andrea Heinz; Qiang Fan; Shuling Guo; Brett Monia; Christian E H Schmelzer; Anthony S Weiss; Matthew Batie; Harikrishnan Parameshwaran; Brian M Varisco
Journal:  Am J Respir Cell Mol Biol       Date:  2018-08       Impact factor: 6.914

8.  Airway Epithelial KIF3A Regulates Th2 Responses to Aeroallergens.

Authors:  Premkumar Vummidi Giridhar; Sheila M Bell; Anusha Sridharan; Priya Rajavelu; Joseph A Kitzmiller; Cheng-Lun Na; Matthew Kofron; Eric B Brandt; Mark Ericksen; Anjaparavanda P Naren; Changsuk Moon; Gurjit K Khurana Hershey; Jeffrey A Whitsett
Journal:  J Immunol       Date:  2016-10-28       Impact factor: 5.422

9.  Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis.

Authors:  Yan Xu; Takako Mizuno; Anusha Sridharan; Yina Du; Minzhe Guo; Jie Tang; Kathryn A Wikenheiser-Brokamp; Anne-Karina T Perl; Vincent A Funari; Jason J Gokey; Barry R Stripp; Jeffrey A Whitsett
Journal:  JCI Insight       Date:  2016-12-08

10.  Interleukin 1 beta and Matrix Metallopeptidase 3 Contribute to Development of Epidermal Growth Factor Receptor-Dependent Serrated Polyps in Mouse Cecum.

Authors:  Zhengxiang He; Lili Chen; Grace Chen; Paola Smaldini; Gerold Bongers; Jovani Catalan-Dibene; Glaucia C Furtado; Sergio A Lira
Journal:  Gastroenterology       Date:  2019-08-27       Impact factor: 22.682

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