Gene Regulatory Network Inference Method Research Articles

COFFEE: consensus single cell-type specific inference for gene regulatory networks.

The inference of gene regulatory networks (GRNs) is crucial to understanding the regulatory mechanisms that govern biological processes. GRNs may be represented as edges in a graph, and hence, it have been inferred computationally for scRNA-seq data. A wisdom of crowds approach to integrate edges from several GRNs to create one composite GRN has demonstrated improved performance when compared with individual algorithm implementations on bulk RNA-seq and microarray data. In an effort to extend this approach to scRNA-seq data, we present COFFEE (COnsensus single cell-type speciFic inFerence for gEnE regulatory networks), a Borda voting-based consensus algorithm that integrates information from 10 established GRN inference methods. We conclude that COFFEE has improved performance across synthetic, curated, and experimental datasets when compared with baseline methods. Additionally, we show that a modified version of COFFEE can be leveraged to improve performance on newer cell-type specific GRN inference methods. Overall, our results demonstrate that consensus-based methods with pertinent modifications continue to be valuable for GRN inference at the single cell level. While COFFEE is benchmarked on 10 algorithms, it is a flexible strategy that can incorporate any set of GRN inference algorithms according to user preference. A Python implementation of COFFEE may be found on GitHub: https://github.com/lodimk2/coffee.

Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP.

Deciphering the underlying gene regulatory networks (GRNs) that govern early human embryogenesis is critical for understanding developmental mechanisms yet remains challenging due to limited sample availability and the inherent complexity of the biological processes involved. To address this, we developed InPheRNo-ChIP, a computational framework that integrates multimodal data, including RNA-seq, transcription factor (TF)-specific ChIP-seq, and phenotypic labels, to reconstruct phenotype-relevant GRNs associated with endoderm development. The core of this method is a probabilistic graphical model that models the simultaneous effect of TFs on their putative target genes to influence a particular phenotypic outcome. Unlike the majority of existing GRN inference methods that are agnostic to the phenotypic outcomes, InPheRNo-ChIP directly incorporates phenotypic information during GRN inference, enabling the distinction between lineage-specific and general regulatory interactions. We integrated data from three experimental studies and applied InPheRNo-ChIP to infer the GRN governing the differentiation of human embryonic stem cells into definitive endoderm. Benchmarking against a scRNA-seq CRISPRi study demonstrated InPheRNo-ChIP's ability to identify regulatory interactions involving endoderm markers FOXA2, SMAD2, and SOX17, outperforming other methods. This highlights the importance of incorporating the phenotypic context during network inference. Furthermore, an ablation study confirms the synergistic contribution of ChIP-seq, RNA-seq, and phenotypic data, highlighting the value of multimodal integration for accurate phenotype-relevant GRN reconstruction.

Inference of gene regulatory networks based on directed graph convolutional networks.

Inferring gene regulatory network (GRN) is one of the important challenges in systems biology, and many outstanding computational methods have been proposed; however there remains some challenges especially in real datasets. In this study, we propose Directed Graph Convolutional neural network-based method for GRN inference (DGCGRN). To better understand and process the directed graph structure data of GRN, a directed graph convolutional neural network is conducted which retains the structural information of the directed graph while also making full use of neighbor node features. The local augmentation strategy is adopted in graph neural network to solve the problem of poor prediction accuracy caused by a large number of low-degree nodes in GRN. In addition, for real data such as E.coli, sequence features are obtained by extracting hidden features using Bi-GRU and calculating the statistical physicochemical characteristics of gene sequence. At the training stage, a dynamic update strategy is used to convert the obtained edge prediction scores into edge weights to guide the subsequent training process of the model. The results on synthetic benchmark datasets and real datasets show that the prediction performance of DGCGRN is significantly better than existing models. Furthermore, the case studies on bladder uroepithelial carcinoma and lung cancer cells also illustrate the performance of the proposed model.

DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations.

Inferring gene regulatory networks (GRNs) allows us to obtain a deeper understanding of cellular function and disease pathogenesis. Recent advances in single-cell RNA sequencing (scRNA-seq) technology have improved the accuracy of GRN inference. However, many methods for inferring individual GRNs from scRNA-seq data are limited because they overlook intercellular heterogeneity and similarities between different cell subpopulations, which are often present in the data. Here, we propose a deep learning-based framework, DeepGRNCS, for jointly inferring GRNs across cell subpopulations. We follow the commonly accepted hypothesis that the expression of a target gene can be predicted based on the expression of transcription factors (TFs) due to underlying regulatory relationships. We initially processed scRNA-seq data by discretizing data scattering using the equal-width method. Then, we trained deep learning models to predict target gene expression from TFs. By individually removing each TF from the expression matrix, we used pre-trained deep model predictions to infer regulatory relationships between TFs and genes, thereby constructing the GRN. Our method outperforms existing GRN inference methods for various simulated and real scRNA-seq datasets. Finally, we applied DeepGRNCS to non-small cell lung cancer scRNA-seq data to identify key genes in each cell subpopulation and analyzed their biological relevance. In conclusion, DeepGRNCS effectively predicts cell subpopulation-specific GRNs. The source code is available at https://github.com/Nastume777/DeepGRNCS.

GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks

We introduce GRouNdGAN, a gene regulatory network (GRN)-guided reference-based causal implicit generative model for simulating single-cell RNA-seq data, in silico perturbation experiments, and benchmarking GRN inference methods. Through the imposition of a user-defined GRN in its architecture, GRouNdGAN simulates steady-state and transient-state single-cell datasets where genes are causally expressed under the control of their regulating transcription factors (TFs). Training on six experimental reference datasets, we show that our model captures non-linear TF-gene dependencies and preserves gene identities, cell trajectories, pseudo-time ordering, and technical and biological noise, with no user manipulation and only implicit parameterization. GRouNdGAN can synthesize cells under new conditions to perform in silico TF knockout experiments. Benchmarking various GRN inference algorithms reveals that GRouNdGAN effectively bridges the existing gap between simulated and biological data benchmarks of GRN inference algorithms, providing gold standard ground truth GRNs and realistic cells corresponding to the biological system of interest.

PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization.

Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates.

Inference of Gene Regulatory Networks Based on Multi-view Hierarchical Hypergraphs.

Since gene regulation is a complex process in which multiple genes act simultaneously, accurately inferring gene regulatory networks (GRNs) is a long-standing challenge in systems biology. Although graph neural networks can formally describe intricate gene expression mechanisms, current GRN inference methods based on graph learning regard only transcription factor (TF)-target gene interactions as pairwise relationships, and cannot model the many-to-many high-order regulatory patterns that prevail among genes. Moreover, these methods often rely on limited prior regulatory knowledge, ignoring the structural information of GRNs in gene expression profiles. Therefore, we propose a multi-view hierarchical hypergraphs GRN (MHHGRN) inference model. Specifically, multiple heterogeneous biological information is integrated to construct multi-view hierarchical hypergraphs of TFs and target genes, using hypergraph convolution networks to model higher order complex regulatory relationships. Meanwhile, the coupled information diffusion mechanism and the cross-domain messaging mechanism facilitate the information sharing between genes to optimise gene embedding representations. Finally, a unique channel attention mechanism is used to adaptively learn feature representations from multiple views for GRN inference. Experimental results show that MHHGRN achieves better results than the baseline methods on the E. coli and S. cerevisiae benchmark datasets of the DREAM5 challenge, and it has excellent cross-species generalization, achieving comparable or better performance on scRNA-seq datasets from five mouse and two human cell lines.

Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference

BackgroundModeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of genome-wide transcription factor activity (TFA) making it difficult to separate covariance and regulatory interactions. Inference of regulatory interactions and TFA requires aggregation of complementary evidence. Estimating TFA explicitly is problematic as it disconnects GRN inference and TFA estimation and is unable to account for, for example, contextual transcription factor-transcription factor interactions, and other higher order features. Deep-learning offers a potential solution, as it can model complex interactions and higher-order latent features, although does not provide interpretable models and latent features.ResultsWe propose a novel autoencoder-based framework, StrUcture Primed Inference of Regulation using latent Factor ACTivity (SupirFactor) for modeling, and a metric, explained relative variance (ERV), for interpretation of GRNs. We evaluate SupirFactor with ERV in a wide set of contexts. Compared to current state-of-the-art GRN inference methods, SupirFactor performs favorably. We evaluate latent feature activity as an estimate of TFA and biological function in S. cerevisiae as well as in peripheral blood mononuclear cells (PBMC).ConclusionHere we present a framework for structure-primed inference and interpretation of GRNs, SupirFactor, demonstrating interpretability using ERV in multiple biological and experimental settings. SupirFactor enables TFA estimation and pathway analysis using latent factor activity, demonstrated here on two large-scale single-cell datasets, modeling S. cerevisiae and PBMC. We find that the SupirFactor model facilitates biological analysis acquiring novel functional and regulatory insight.

Deep Learning in Gene Regulatory Network Inference: A Survey.

Understanding the intricate regulatory relationships among genes is crucial for comprehending the development, differentiation, and cellular response in living systems. Consequently, inferring gene regulatory networks (GRNs) based on observed data has gained significant attention as a fundamental goal in biological applications. The proliferation and diversification of available data present both opportunities and challenges in accurately inferring GRNs. Deep learning, a highly successful technique in various domains, holds promise in aiding GRN inference. Several GRN inference methods employing deep learning models have been proposed; however, the selection of an appropriate method remains a challenge for life scientists. In this survey, we provide a comprehensive analysis of 12 GRN inference methods that leverage deep learning models. We trace the evolution of these major methods and categorize them based on the types of applicable data. We delve into the core concepts and specific steps of each method, offering a detailed evaluation of their effectiveness and scalability across different scenarios. These insights enable us to make informed recommendations. Moreover, we explore the challenges faced by GRN inference methods utilizing deep learning and discuss future directions, providing valuable suggestions for the advancement of data scientists in this field.

Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer.

Gene regulatory networks (GRNs) and gene co-expression networks (GCNs) allow genome-wide exploration of molecular regulation patterns in health and disease. The standard approach for obtaining GRNs and GCNs is to infer them from gene expression data, using computational network inference methods. However, since network inference methods are usually applied on aggregate data, distortion of the networks by demographic confounders might remain undetected, especially because gene expression patterns are known to vary between different demographic groups. In this paper, we present a computational framework to systematically evaluate the influence of demographic confounders on network inference from gene expression data. Our framework compares similarities between networks inferred for different demographic groups with similarity distributions obtained for random splits of the expression data. Moreover, it allows to quantify to which extent demographic groups are represented by networks inferred from the aggregate data in a confounder-agnostic way. We apply our framework to test four widely used GRN and GCN inference methods as to their robustness w. r. t. confounding by age, ethnicity and sex in cancer. Our findings based on more than $ {44000}$ inferred networks indicate that age and sex confounders play an important role in network inference for certain cancer types, emphasizing the importance of incorporating an assessment of the effect of demographic confounders into network inference workflows. Our framework is available as a Python package on GitHub: https://github.com/bionetslab/grn-confounders.

Inferring single-cell gene regulatory network by non-redundant mutual information.

Gene regulatory network plays a crucial role in controlling the biological processes of living creatures. Deciphering the complex gene regulatory networks from experimental data remains a major challenge in system biology. Recent advances in single-cell RNA sequencing technology bring massive high-resolution data, enabling computational inference of cell-specific gene regulatory networks (GRNs). Many relevant algorithms have been developed to achieve this goal in the past years. However, GRN inference is still less ideal due to the extra noises involved in pseudo-time information and large amounts of dropouts in datasets. Here, we present a novel GRN inference method named Normi, which is based on non-redundant mutual information. Normi manipulates these problems by employing a sliding size-fixed window approach on the entire trajectory and conducts average smoothing strategy on the gene expression of the cells in each window to obtain representative cells. To further alleviate the impact of dropouts, we utilize the mixed KSG estimator to quantify the high-order time-delayed mutual information among genes, then filter out the redundant edges by adopting Max-Relevance and Min Redundancy algorithm. Moreover, we determined the optimal time delay for each gene pair by distance correlation. Normi outperforms other state-of-the-art GRN inference methods on both simulated data and single-cell RNA sequencing (scRNA-seq) datasets, demonstrating its superiority in robustness. The performance of Normi in real scRNA-seq data further reveals its ability to identify the key regulators and crucial biological processes.

Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model.

The gene regulatory structure of cells involves not only the regulatory relationship between two genes, but also the cooperative associations of multiple genes. However, most gene regulatory network inference methods for single cell only focus on and infer the regulatory relationships of pairs of genes, ignoring the global regulatory structure which is crucial to identify the regulations in the complex biological systems. Here, we proposed a graph-based Deep learning model for Regulatory networks Inference among Genes (DeepRIG) from single-cell RNA-seq data. To learn the global regulatory structure, DeepRIG builds a prior regulatory graph by transforming the gene expression of data into the co-expression mode. Then it utilizes a graph autoencoder model to embed the global regulatory information contained in the graph into gene latent embeddings and to reconstruct the gene regulatory network. Extensive benchmarking results demonstrate that DeepRIG can accurately reconstruct the gene regulatory networks and outperform existing methods on multiple simulated networks and real-cell regulatory networks. Additionally, we applied DeepRIG to the samples of human peripheral blood mononuclear cells and triple-negative breast cancer, and presented that DeepRIG can provide accurate cell-type-specific gene regulatory networks inference and identify novel regulators of progression and inhibition.

Ensemble Learning Based Gene Regulatory Network Inference

In the machine learning field, the technique known as ensemble learning aims at combining different base learners in order to increase the quality and the robustness of the predictions. Indeed, this approach has widely been applied to tackle, with success, real world problems from different domains, including computational biology. Nevertheless, despite their potential, ensembles combining results from different base learners have been understudied in the context of gene regulatory network inference. In this paper we applied genetic algorithms and frequent itemset mining, to design small but effective ensembles of gene regulatory network inference methods. These ensembles were evaluated and compared to well-established single and ensemble methods, on both real and synthetic datasets. Results showed that small ensembles, consisting of few but diverse base learners, enhance the exploration of the solution space, and compensate base learners biases, outperforming state-of-the-art methods. Results advocate for the use of such methods as gene regulatory network inference tools.

LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data.

From a systematic perspective, it is crucial to infer and analyze gene regulatory network (GRN) from high-throughput single-cell RNA sequencing data. However, most existing GRN inference methods mainly focus on the network topology, only few of them consider how to explicitly describe the updated logic rules of regulation in GRNs to obtain their dynamics. Moreover, some inference methods also fail to deal with the over-fitting problem caused by the noise in time series data. In this article, we propose a novel embedded Boolean threshold network method called LogBTF, which effectively infers GRN by integrating regularized logistic regression and Boolean threshold function. First, the continuous gene expression values are converted into Boolean values and the elastic net regression model is adopted to fit the binarized time series data. Then, the estimated regression coefficients are applied to represent the unknown Boolean threshold function of the candidate Boolean threshold network as the dynamical equations. To overcome the multi-collinearity and over-fitting problems, a new and effective approach is designed to optimize the network topology by adding a perturbation design matrix to the input data and thereafter setting sufficiently small elements of the output coefficient vector to zeros. In addition, the cross-validation procedure is implemented into the Boolean threshold network model framework to strengthen the inference capability. Finally, extensive experiments on one simulated Boolean value dataset, dozens of simulation datasets, and three real single-cell RNA sequencing datasets demonstrate that the LogBTF method can infer GRNs from time series data more accurately than some other alternative methods for GRN inference. The source data and code are available at https://github.com/zpliulab/LogBTF.

GReNaDIne: A Data-Driven Python Library to Infer Gene Regulatory Networks from Gene Expression Data.

Context: Inferring gene regulatory networks (GRN) from high-throughput gene expression data is a challenging task for which different strategies have been developed. Nevertheless, no ever-winning method exists, and each method has its advantages, intrinsic biases, and application domains. Thus, in order to analyze a dataset, users should be able to test different techniques and choose the most appropriate one. This step can be particularly difficult and time consuming, since most methods' implementations are made available independently, possibly in different programming languages. The implementation of an open-source library containing different inference methods within a common framework is expected to be a valuable toolkit for the systems biology community. Results: In this work, we introduce GReNaDIne (Gene Regulatory Network Data-driven Inference), a Python package that implements 18 machine learning data-driven gene regulatory network inference methods. It also includes eight generalist preprocessing techniques, suitable for both RNA-seq and microarray dataset analysis, as well as four normalization techniques dedicated to RNA-seq. In addition, this package implements the possibility to combine the results of different inference tools to form robust and efficient ensembles. This package has been successfully assessed under the DREAM5 challenge benchmark dataset. The open-source GReNaDIne Python package is made freely available in a dedicated GitLab repository, as well as in the official third-party software repository PyPI Python Package Index. The latest documentation on the GReNaDIne library is also available at Read the Docs, an open-source software documentation hosting platform. Contribution: The GReNaDIne tool represents a technological contribution to the field of systems biology. This package can be used to infer gene regulatory networks from high-throughput gene expression data using different algorithms within the same framework. In order to analyze their datasets, users can apply a battery of preprocessing and postprocessing tools and choose the most adapted inference method from the GReNaDIne library and even combine the output of different methods to obtain more robust results. The results format provided by GReNaDIne is compatible with well-known complementary refinement tools such as PYSCENIC.

Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes.

Accurate determination of causalities between genes is a challenge in the inference of gene regulatory networks (GRNs) from the gene expression profile. Although many methods have been developed for the reconstruction of GRNs, most of them are insufficient in determining causalities or regulatory directions. In this work, we present a novel method, namely, DDTG, to improve the accuracy of causality determination in GRN inference by dissecting downstream target genes. In the proposed method, the topology and hierarchy of GRNs are determined by mutual information and conditional mutual information, and the regulatory directions of GRNs are determined by Taylor formula-based regression. In addition, indirect interactions are removed with the sparseness of the network topology to improve the accuracy of network inference. The method is validated on the benchmark GRNs from DREAM3 and DREAM4 challenges. The results demonstrate the superior performance of the DDTG method on causality determination of GRNs compared to some popular GRN inference methods. This work provides a useful tool to infer the causal gene regulatory network.

Knowledge of the perturbation design is essential for accurate gene regulatory network inference

The gene regulatory network (GRN) of a cell executes genetic programs in response to environmental and internal cues. Two distinct classes of methods are used to infer regulatory interactions from gene expression: those that only use observed changes in gene expression, and those that use both the observed changes and the perturbation design, i.e. the targets used to cause the changes in gene expression. Considering that the GRN by definition converts input cues to changes in gene expression, it may be conjectured that the latter methods would yield more accurate inferences but this has not previously been investigated. To address this question, we evaluated a number of popular GRN inference methods that either use the perturbation design or not. For the evaluation we used targeted perturbation knockdown gene expression datasets with varying noise levels generated by two different packages, GeneNetWeaver and GeneSpider. The accuracy was evaluated on each dataset using a variety of measures. The results show that on all datasets, methods using the perturbation design matrix consistently and significantly outperform methods not using it. This was also found to be the case on a smaller experimental dataset from E. coli. Targeted gene perturbations combined with inference methods that use the perturbation design are indispensable for accurate GRN inference.

PGRNIG: novel parallel gene regulatory network identification algorithm based on GPU.

Molecular biology has revealed that complex life phenomena can be treated as the result of many gene interactions. Investigating these interactions and understanding the intrinsic mechanisms of biological systems using gene expression data have attracted a lot of attention. As a typical gene regulatory network (GRN) inference method, the S-system has been utilized to deal with small-scale network identification. However, it is extremely difficult to optimize it to infer medium-to-large networks. This paper proposes a novel parallel swarm intelligent algorithm, PGRNIG, to optimize the parameters of the S-system. We employed the clone selection strategy to improve the whale optimization algorithm (CWOA). To enhance the time efficiency of CWOA optimization, we utilized a parallel CWOA (PCWOA) based on the compute unified device architecture (CUDA) platform. Decomposition strategy and L1 regularization were utilized to reduce the search space and complexity of GRN inference. We applied the PGRNIG algorithm on three synthetic datasets and two real time-series expression datasets of the species of Escherichia coli and Saccharomyces cerevisiae. Experimental results show that PGRNIG could infer the gene regulatory network more accurately than other state-of-the-art methods with a convincing computational speed-up. Our findings show that CWOA and PCWOA have faster convergence performances than WOA.

Optimal Sparsity Selection Based on an Information Criterion for Accurate Gene Regulatory Network Inference.

Accurate inference of gene regulatory networks (GRNs) is important to unravel unknown regulatory mechanisms and processes, which can lead to the identification of treatment targets for genetic diseases. A variety of GRN inference methods have been proposed that, under suitable data conditions, perform well in benchmarks that consider the entire spectrum of false-positives and -negatives. However, it is very challenging to predict which single network sparsity gives the most accurate GRN. Lacking criteria for sparsity selection, a simplistic solution is to pick the GRN that has a certain number of links per gene, which is guessed to be reasonable. However, this does not guarantee finding the GRN that has the correct sparsity or is the most accurate one. In this study, we provide a general approach for identifying the most accurate and sparsity-wise relevant GRN within the entire space of possible GRNs. The algorithm, called SPA, applies a “GRN information criterion” (GRNIC) that is inspired by two commonly used model selection criteria, Akaike and Bayesian Information Criterion (AIC and BIC) but adapted to GRN inference. The results show that the approach can, in most cases, find the GRN whose sparsity is close to the true sparsity and close to as accurate as possible with the given GRN inference method and data. The datasets and source code can be found at https://bitbucket.org/sonnhammergrni/spa/.

GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.

Accurate inference of gene regulatory networks (GRN) is an essential component of systems biology, and there is a constant development of new inference methods. The most common approach to assess accuracy for publications is to benchmark the new method against a selection of existing algorithms. This often leads to a very limited comparison, potentially biasing the results, which may stem from tuning the benchmark's properties or incorrect application of other methods. These issues can be avoided by a web server with a broad range of data properties and inference algorithms, that makes it easy to perform comprehensive benchmarking of new methods, and provides a more objective assessment. Here we present https://GRNbenchmark.org/ - a new web server for benchmarking GRN inference methods, which provides the user with a set of benchmarks with several datasets, each spanning a range of properties including multiple noise levels. As soon as the web server has performed the benchmarking, the accuracy results are made privately available to the user via interactive summary plots and underlying curves. The user can then download these results for any purpose, and decide whether or not to make them public to share with the community.