scholarly journals Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks

2016 ◽  
Vol 113 (16) ◽  
pp. 4290-4295 ◽  
Author(s):  
Siqi Wu ◽  
Antony Joseph ◽  
Ann S. Hammonds ◽  
Susan E. Celniker ◽  
Bin Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Matrix Factorization ◽  
Gene Networks ◽  
Regulatory Networks ◽  
Nonnegative Matrix Factorization ◽  
Expression Patterns ◽  
Selection Criterion ◽  
Nonnegative Matrix ◽  
Biological Information ◽  
Expression Data

Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set of Drosophila early embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation of Drosophila expression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior–posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. The performance of PP with the Drosophila data suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

Matrix Factorization-based Improved Classification of Gene Expression Data

2020 ◽  
Vol 13 (5) ◽  
pp. 858-863
Author(s):  
Shaily Malik ◽  
Poonam Bansal
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Matrix Factorization ◽  
Latent Dirichlet Allocation ◽  
Nonnegative Matrix ◽  
Biological Information ◽  
Support Vector ◽  
Expression Data ◽  
Data Set ◽  
Nonnegativity Constraints

Background: The medical data, in the form of prescriptions and test reports, is very extensive which needs a comprehensive analysis. Objective: The gene expression data set is formulated using a very large number of genes associated to thousands of samples. Identifying the relevant biological information from these complex associations is a difficult task. Methods: For this purpose, a variety of classification algorithms are available which can be used to automatically detect the desired information. K-Nearest Neighbour Algorithm, Latent Dirichlet Allocation, Gaussian Naïve Bayes and support Vector Classifier are some of the well known algorithms used for the classification task. Nonnegative Matrix Factorization is a technique which has gained a lot of popularity because of its nonnegativity constraints. This technique can be used for better interpretability of data. Results: In this paper, we applied NMF as a pre-processing step for better results. We also evaluated the given classifiers on the basis of four criteria: accuracy, precision, specificity and Recall. Conclusion: The experimental results shows that these classifiers give better performance when NMF is applied at pre-processing of data before giving it to the said classifiers. Gaussian Naïve Bias algorithm showed a significant improvement in classification after the application of NMF at preprocessing.

Building Gene Networks by Analyzing Gene Expression Profiles

2019 ◽  
pp. 27-44
Author(s):  
Crescenzio Gallo
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Networks ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Expression Data ◽  
Gene Expressions ◽  
Over Time

The possible applications of modeling and simulation in the field of bioinformatics are very extensive, ranging from understanding basic metabolic paths to exploring genetic variability. Experimental results carried out with DNA microarrays allow researchers to measure expression levels for thousands of genes simultaneously, across different conditions and over time. A key step in the analysis of gene expression data is the detection of groups of genes that manifest similar expression patterns. In this chapter, the authors examine various methods for analyzing gene expression data, addressing the important topics of (1) selecting the most differentially expressed genes, (2) grouping them by means of their relationships, and (3) classifying samples based on gene expressions.

scholarly journals Limit cycle dynamics can guide the evolution of gene regulatory networks towards point attractors

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stuart P. Wilson ◽  
Sebastian S. James ◽  
Daniel J. Whiteley ◽  
Leah A. Krubitzer
Keyword(s):  
Gene Expression ◽  
Limit Cycles ◽  
Gene Networks ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Specific Gene ◽  
Boolean Models ◽  
A Genome ◽  
Order Of Magnitude ◽  
Accelerate Evolution

AbstractDevelopmental dynamics in Boolean models of gene networks self-organize, either into point attractors (stable repeating patterns of gene expression) or limit cycles (stable repeating sequences of patterns), depending on the network interactions specified by a genome of evolvable bits. Genome specifications for dynamics that can map specific gene expression patterns in early development onto specific point attractor patterns in later development are essentially impossible to discover by chance mutation alone, even for small networks. We show that selection for approximate mappings, dynamically maintained in the states comprising limit cycles, can accelerate evolution by at least an order of magnitude. These results suggest that self-organizing dynamics that occur within lifetimes can, in principle, guide natural selection across lifetimes.

CURVE-BASED CLUSTERING OF TIME COURSE GENE EXPRESSION DATA USING SELF-ORGANIZING MAPS

2009 ◽  
Vol 07 (04) ◽  
pp. 645-661 ◽  
Author(s):  
XIN CHEN
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Regulatory Networks ◽  
Time Course ◽  
Clustering Algorithm ◽  
Expression Patterns ◽  
Self Organizing Map ◽  
Expression Data ◽  
Wide Range ◽  
Self Organizing

There is an increasing interest in clustering time course gene expression data to investigate a wide range of biological processes. However, developing a clustering algorithm ideal for time course gene express data is still challenging. As timing is an important factor in defining true clusters, a clustering algorithm shall explore expression correlations between time points in order to achieve a high clustering accuracy. Moreover, inter-cluster gene relationships are often desired in order to facilitate the computational inference of biological pathways and regulatory networks. In this paper, a new clustering algorithm called CurveSOM is developed to offer both features above. It first presents each gene by a cubic smoothing spline fitted to the time course expression profile, and then groups genes into clusters by applying a self-organizing map-based clustering on the resulting splines. CurveSOM has been tested on three well-studied yeast cell cycle datasets, and compared with four popular programs including Cluster 3.0, GENECLUSTER, MCLUST, and SSClust. The results show that CurveSOM is a very promising tool for the exploratory analysis of time course expression data, as it is not only able to group genes into clusters with high accuracy but also able to find true time-shifted correlations of expression patterns across clusters.

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