scholarly journals Molecular characterization of gene regulatory networks in primary human tracheal and bronchial epithelial cells

2018 ◽  
Vol 17 (4) ◽  
pp. 444-453 ◽  
Author(s):  
Austin E. Gillen ◽  
Rui Yang ◽  
Calvin U. Cotton ◽  
Aura Perez ◽  
Scott H. Randell ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Molecular Characterization ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Bronchial Epithelial Cells ◽  
Bronchial Epithelial ◽  
Gene Regulatory

scholarly journals Cell cycle alterations induced by urban PM2.5 in bronchial epithelial cells: characterization of the process and possible mechanisms involved

2013 ◽  
Vol 10 (1) ◽  
pp. 63 ◽  
Author(s):  
Eleonora Longhin ◽  
Jørn A Holme ◽  
Kristine B Gutzkow ◽  
Volker M Arlt ◽  
Jill E Kucab ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Epithelial Cells ◽  
Bronchial Epithelial Cells ◽  
Bronchial Epithelial ◽  
Cell Cycle Alterations

scholarly journals Integration of a Computational Pipeline for Dynamic Inference of Gene Regulatory Networks in Single Cells

2019 ◽  
Author(s):  
Kyung Dae Ko ◽  
Stefania Dell’Orso ◽  
Aster H. Juan ◽  
Vittorio Sartorelli
Keyword(s):  
Prior Knowledge ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Developmental Stages ◽  
Individual Cell ◽  
Single Cells ◽  
Rna Seq ◽  
Gene Regulatory ◽  
Molecular Expression

SUMMARYSingle-cell RNA-seq permits the characterization of the molecular expression states of individual cells. Several methods have been developed to spatially and temporally resolve individual cell populations. However, these methods are not always integrated and some of them are constrained by prior knowledge. Here, we present an integrated pipeline for inference of gene regulatory networks. The pipeline does not rely on prior knowledge, it improves inference accuracy by integrating signatures from different data dimensions and facilitates tracing variation of gene expression by visualizing gene-interacting patterns of co-expressed gene regulatory networks at distinct developmental stages.

scholarly journals Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation

2006 ◽  
Vol 27 (2) ◽  
pp. 141-155 ◽  
Author(s):  
Anders Stegmann ◽  
Morten Hansen ◽  
Yulan Wang ◽  
Janus B. Larsen ◽  
Leif R. Lund ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Epithelial Cells ◽  
Gene Regulatory Networks ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Intestinal Epithelial ◽  
Gene Regulatory ◽  
Small Intestinal

DNA-binding transcription factors bind to promoters that carry their binding sites. Transcription factors therefore function as nodes in gene regulatory networks. In the present work we used a bioinformatic approach to search for transcription factors that might function as nodes in gene regulatory networks during the differentiation of the small intestinal epithelial cell. In addition we have searched for connections between transcription factors and the villus metabolome. Transcriptome data were generated from mouse small intestinal villus, crypt, and fetal intestinal epithelial cells. Metabolome data were generated from crypt and villus cells. Our results show that genes that are upregulated during fetal to adult and crypt to villus differentiation have an overrepresentation of potential hepatocyte nuclear factor (HNF)-4 binding sites in their promoters. Moreover, metabolome analyses by magic angle spinning 1H nuclear magnetic resonance spectroscopy showed that the villus epithelial cells contain higher concentrations of lipid carbon chains than the crypt cells. These findings suggest a model where the HNF-4 transcription factor influences the villus metabolome by regulating genes that are involved in lipid metabolism. Our approach also identifies transcription factors of importance for crypt functions such as DNA replication (E2F) and stem cell maintenance (c-Myc).

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