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 Inferring gene regulatory networks from single-cell RNA-seq temporal snapshot data requires higher-order moments

Patterns ◽  
2021 ◽  
Vol 2 (9) ◽  
pp. 100332
Author(s):  
N. Alexia Raharinirina ◽  
Felix Peppert ◽  
Max von Kleist ◽  
Christof Schütte ◽  
Vikram Sunkara
Keyword(s):  
Single Cell ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Higher Order ◽  
Rna Seq ◽  
Higher Order Moments ◽  
Gene Regulatory

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 Characterization of rare spindle and root cell transcriptional profiles in the stria vascularis of the adult mouse cochlea

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shoujun Gu ◽  
Rafal Olszewski ◽  
Ian Taukulis ◽  
Zheng Wei ◽  
Daniel Martin ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Adult Mouse ◽  
Stria Vascularis ◽  
Cell Types ◽  
Rna Seq ◽  
Root Cells ◽  
Transcriptional Profiles ◽  
Gene Regulatory

Abstract The stria vascularis (SV) in the cochlea generates and maintains the endocochlear potential, thereby playing a pivotal role in normal hearing. Knowing transcriptional profiles and gene regulatory networks of SV cell types establishes a basis for studying the mechanism underlying SV-related hearing loss. While we have previously characterized the expression profiles of major SV cell types in the adult mouse, transcriptional profiles of rare SV cell types remained elusive due to the limitation of cell capture in single-cell RNA-Seq. The role of these rare cell types in the homeostatic function of the adult SV remain largely undefined. In this study, we performed single-nucleus RNA-Seq on the adult mouse SV in conjunction with sample preservation treatments during the isolation steps. We distinguish rare SV cell types, including spindle cells and root cells, from other cell types, and characterize their transcriptional profiles. Furthermore, we also identify and validate novel specific markers for these rare SV cell types. Finally, we identify homeostatic gene regulatory networks within spindle and root cells, establishing a basis for understanding the functional roles of these cells in hearing. These novel findings will provide new insights for future work in SV-related hearing loss and hearing fluctuation.

scholarly journals Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge

2007 ◽  
Vol 6 (1) ◽  
Author(s):  
Adriano V Werhli ◽  
Dirk Husmeier
Keyword(s):  
Prior Knowledge ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Reconstruction Error ◽  
Expression Data ◽  
Multiple Sources ◽  
Promoter Regions ◽  
Experimental Conditions ◽  
Microarray Expression Data ◽  
Gene Regulatory

There have been various attempts to reconstruct gene regulatory networks from microarray expression data in the past. However, owing to the limited amount of independent experimental conditions and noise inherent in the measurements, the results have been rather modest so far. For this reason it seems advisable to include biological prior knowledge, related, for instance, to transcription factor binding locations in promoter regions or partially known signalling pathways from the literature. In the present paper, we consider a Bayesian approach to systematically integrate expression data with multiple sources of prior knowledge. Each source is encoded via a separate energy function, from which a prior distribution over network structures in the form of a Gibbs distribution is constructed. The hyperparameters associated with the different sources of prior knowledge, which measure the influence of the respective prior relative to the data, are sampled from the posterior distribution with MCMC. We have evaluated the proposed scheme on the yeast cell cycle and the Raf signalling pathway. Our findings quantify to what extent the inclusion of independent prior knowledge improves the network reconstruction accuracy, and the values of the hyperparameters inferred with the proposed scheme were found to be close to optimal with respect to minimizing the reconstruction error.

scholarly journals Characterization of eyes, photoreceptors and opsins in developmental stages of the chaetognath Spadella cephaloptera

2019 ◽  
Author(s):  
Tim Wollesen ◽  
Sonia Victoria Rodríguez Monje ◽  
Adam Phillip Oel ◽  
Detlev Arendt
Keyword(s):  
Regulatory Networks ◽  
Developmental Stages ◽  
Photoreceptor Cells ◽  
Phylogenetic Position ◽  
Developmental Studies ◽  
Head Region ◽  
Platynereis Dumerilii ◽  
Spadella Cephaloptera ◽  
Gene Regulatory

AbstractThe phylogenetic position of chaetognaths has been debated for decades, however recently they have been grouped into the Gnathifera, sister taxon to the Lophotrochozoa. Chaetognaths possess photoreceptor cells that are anatomically unique and arranged remarkably different in the eyes of the various species. Studies investigating eye development and underlying gene regulatory networks are so far missing.In order to gain insights into the development and the molecular toolkit of chaetognath photoreceptors and eyes a new transcriptome of the epibenthic species Spadella cephaloptera was searched for opsins. Our screen revealed single-copies of xenopsin and peropsin and gene expression analyses demonstrated that only xenopsin is expressed in photoreceptor cells of the developing lateral eyes. Adults likewise exhibit two xenopsin+ photoreceptor cells in each of their lateral eyes. Beyond that, a single cryptochrome gene was uncovered and found co-expressed with xenopsin in some photoreceptor cells of the lateral developing eye. In addition, it is co-expressed with peropsin in the cerebral ganglia, a condition reminiscent of a non-visual photoreceptive zone in the apical nervous system of the annelid Platynereis dumerilii that performs circadian entrainment and melatonin release. Cryptochrome expression was also detected in cells of the corona ciliata, a circular organ in the posterior dorsal head region that has been attributed several functions arguing for an involvement of this organ in circadian entrainment. Our study demonstrates the importance to investigate representatives of the Gnathifera, a clade that has been neglected with respect to developmental studies and that might contribute to unravel the evolution of spiralian and bilaterian body plans.

scholarly journals A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets

2016 ◽  
Vol 12 (06) ◽  
pp. 340-341 ◽  
Author(s):  
Fereshteh Izadi ◽  
◽  
Hamid Najafi Zarrini ◽  
Nadali Babaeian Jelodar ◽  
◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Rna Seq ◽  
Gene Regulatory ◽  
Analytical Assay
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