Application of Multilayer Network Models in Bioinformatics

Alterations in the multilayer network in patients with rapid eye movement sleep behaviour disorder

This study aimed to reveal the pathophysiology of isolated rapid eye movement sleep behaviour disorder (RBD) in patients using multilayer network analysis. Participants eligible for isolated RBD were included and verified via polysomnography. Both iRBD patients and healthy controls underwent brain MRI, including T1-weighted imaging and diffusion tensor imaging. Grey matter matrix was derived from T1-weighted images using a morphometric similarity network. White matter matrix was formed from diffusion tensor imaging-based structural connectivity. Multilayer network analysis of grey and white matter was performed using graph theory. We studied 29 isolated RBD patients and 30 healthy controls. Patients exhibited a higher average overlap degree (27.921 vs. 23.734, p = 0.002) and average multilayer clustering coefficient (0.474 vs. 0.413, p = 0.002) compared with controls. Additionally, several regions showed significant differences in the degree of overlap and multilayer clustering coefficient between patients with isolated RBD and healthy controls at the nodal level. The degree of overlap in the left medial orbitofrontal, left posterior cingulate, and right paracentral nodes and the multilayer clustering coefficients in the left lateral occipital, left rostral middle frontal, right fusiform, right inferior posterior parietal, and right parahippocampal nodes were higher in patients with isolated RBD than in healthy controls. We found alterations in the multilayer network at the global and nodal levels in patients with isolated RBD, and these changes may be associated with the pathophysiology of isolated RBD. Multilayer network analysis can be used widely to explore the mechanisms underlying various neurological disorders.

Multilayer network analysis in patients with juvenile myoclonic epilepsy

INTRODUCTION

We conducted a multilayer network analysis in patients with juvenile myoclonic epilepsy (JME) and healthy controls, to investigate the gray matter layer using a morphometric similarity network and analyze the white matter layer using structural connectivity.

METHODS

We enrolled 42 patients with newly diagnosed JME and 53 healthy controls. Brain magnetic resonance imaging (MRI) using a three-tesla MRI scanner, including T1-weighted imaging and diffusion tensor imaging (DTI) were performed. We created a gray matter layer matrix with a morphometric similarity network using T1-weighted imaging, and a white matter layer matrix with structural connectivity using the DTI. Subsequently, we performed a multilayer network analysis by applying graph theory.

RESULTS

There were significant differences in network at the global level in the multilayer network analysis between the groups. The average multiplex participation of patients with JME was lower than that of healthy controls (0.858 vs. 0.878, p = 0.007). In addition, several regions showed significant differences in multiplex participation at the nodal level in the multilayer network analysis. Multiplex participation in the right entorhinal cortex was lower, whereas multiplex participation in the right supramarginal gyrus was higher at the nodal level in the multilayer network analysis of patients with JME compared to healthy controls.

CONCLUSION

We demonstrated differences in network at the global and nodal levels in the multilayer network analysis between patients with JME and healthy controls. These features may be associated with the pathophysiology of JME and could help us understand the complex brain network in patients with JME.

Alteration of multilayer network perspective on gray and white matter connectivity in obstructive sleep apnea

PURPOSE

The objective of this research was to examine changes in the neural networks of both gray and white matter in individuals with obstructive sleep apnea (OSA) in comparison to those without the condition, employing a comprehensive multilayer network analysis.

METHODS

Patients meeting the criteria for OSA were recruited through polysomnography, while a control group of healthy individuals matched for age and sex was also assembled. Utilizing T1-weighted imaging, a morphometric similarity network was crafted to represent gray matter, while diffusion tensor imaging provided structural connectivity for constructing a white matter network. A multilayer network analysis was then performed, employing graph theory methodologies.

RESULTS

We included 40 individuals diagnosed with OSA and 40 healthy participants in our study. Analysis revealed significant differences in various global network metrics between the two groups. Specifically, patients with OSA exhibited higher average degree overlap and average multilayer clustering coefficient (28.081 vs. 23.407, p < 0.001; 0.459 vs. 0.412, p = 0.004), but lower multilayer modularity (0.150 vs. 0.175, p = 0.001) compared to healthy controls. However, no significant differences were observed in average multiplex participation, average overlapping strength, or average weighted multiplex participation between the patients with OSA and healthy controls. Moreover, several brain regions displayed notable differences in degree overlap at the nodal level between patients with OSA and healthy controls.

CONCLUSION

Remarkable alterations in the multilayer network, indicating shifts in both gray and white matter, were detected in patients with OSA in contrast to their healthy counterparts. Further examination at the nodal level unveiled notable changes in regions associated with cognition, underscoring the effectiveness of multilayer network analysis in exploring interactions across brain layers.

Structural and functional multilayer network analysis in restless legs syndrome patients

The combination of brain structural and functional connectivity offers complementary insights into its organisation. Multilayer network analysis explores various relationships across different layers within a single system. We aimed to investigate changes in the structural and functional multilayer network in 69 patients with primary restless legs syndrome (RLS) compared with 50 healthy controls. Participants underwent diffusion tensor imaging (DTI) and resting state-functional magnetic resonance imaging (rs-fMRI) using a three-tesla MRI scanner. We constructed a structural connectivity matrix derived from DTI using a DSI program and made a functional connectivity matrix based on rs-fMRI using an SPM program and CONN toolbox. A multilayer network analysis, using BRAPH program, was then conducted to assess the connectivity patterns in both groups. At the global level, significant differences there were between the patients with RLS and healthy controls. The average multiplex participation was lower in patients with RLS than in healthy controls (0.804 vs. 0.821, p = 0.042). Additionally, several regions showed significant differences in the nodal level in multiplex participation between patients with RLS and healthy controls, particularly the frontal and temporal lobes. The regions affected included the inferior frontal gyrus, medial orbital gyrus, precentral gyrus, rectus gyrus, insula, superior and inferior temporal gyrus, medial and lateral occipitotemporal gyrus, and temporal pole. These results represent evidence of diversity in interactions between structural and functional connectivity in patients with RLS, providing a more comprehensive understanding of the brain network in RLS. This may contribute to a precise diagnosis of RLS, and aid the development of a biomarker to track treatment effectiveness.

Multilayer network changes in patients with migraine

INTRODUCTION

To investigate changes in the multilayer network in patients with migraine compared to healthy controls.

METHODS

This study enrolled 82 patients with newly diagnosed migraine without aura and 53 healthy controls. Brain magnetic resonance imaging (MRI) was conducted using a 3-tesla MRI scanner, including three-dimensional T1-weighted and diffusion tensor imaging (DTI). A gray matter layer matrix was created with a morphometric similarity network using T1-weighted imaging and the FreeSurfer program. A white matter layer matrix was also created with structural connectivity using the DTI studio (DSI) program. A multilayer network analysis was then performed by applying graph theory using the BRAPH program.

RESULTS

Significant changes were observed in the multilayer network at the global level in patients with migraines compared to the healthy controls. The multilayer modularity (0.177 vs. 0.160, p = .0005) and average multiplex participation (0.934 vs. 0.924, p = .002) were higher in patients with migraines than in the healthy controls. In contrast, the average multilayer clustering coefficient (0.406 vs. 0.461, p = .0005), average overlapping strength (56.061 vs. 61.676, p = .0005), and average weighted multiplex participation (0.847 vs. 0.878, p = .0005) were lower in patients with migraine than in the healthy controls. In addition, several regions showed significant changes in the multilayer network at the nodal level, including multiplex participation, multilayer clustering coefficients, overlapping strengths, and weighted multiplex participation.

CONCLUSION

This study demonstrated significant changes in the multilayer network in patients with migraines compared to healthy controls. This could aid an understanding of the complex brain network in patients with migraine and may be associated with the pathophysiology of migraines. Patients with migraine show multilayer network changes in widespreading brain regions compared to healthy controls, and specific brain areas seem to play a hub role for pathophysiology of the migraine.

Involvement of the default mode network in patients with transient global amnesia: multilayer network

INTRODUCTION

We aimed to investigate the alterations in the multilayer network in patients with transient global amnesia (TGA).

METHODS

We enrolled 124 patients with TGA and 80 healthy controls. Both patients with TGA and healthy controls underwent a three-teslar brain magnetic resonance imaging (MRI). A gray matter layer matrix was created using a morphometric similarity network derived from the T1-weighted imaging, and a white matter layer matrix was constructed using structural connectivity based on the diffusion tensor imaging. A multilayer network analysis was performed by applying graph theoretical analysis.

RESULTS

There were no significant differences in global network measures between the groups. However, several regions, related to the default mode network, showed significant differences in nodal network measures between the groups. Multi-richness in the left pars opercularis, multi-rich-club degree in the right posterior cingulate gyrus, and weighted multiplex participation in the right posterior cingulate gyrus were higher in patients with TGA compared with healthy controls (15.47 vs. 12.26, p = 0.0005; 41.68 vs. 37.16, p = 0.0005; 0.90 vs. 0.80, p = 0.0005; respectively). The multiplex core-periphery in the left precuneus was higher (0.96 vs. 0.84, p = 0.0005), whereas that in the transverse temporal gyrus was lower in patients with TGA compared with healthy controls (0.00 vs. 0.02, p = 0.0005).

CONCLUSION

We newly find the alterations in the multilayer network in patients with TGA compared with healthy controls, which shows the involvement of the default mode network. These changes may be related to the pathophysiology of TGA.

Multilayer network alignment based on topological assessment via embeddings

BACKGROUND

Network graphs allow modelling the real world objects in terms of interactions. In a multilayer network, the interactions are distributed over layers (i.e., intralayer and interlayer edges). Network alignment (NA) is a methodology that allows mapping nodes between two or multiple given networks, by preserving topologically similar regions. For instance, NA can be applied to transfer knowledge from one biological species to another. In this paper, we present DANTEml, a software tool for the Pairwise Global NA (PGNA) of multilayer networks, based on topological assessment. It builds its own similarity matrix by processing the node embeddings computed from two multilayer networks of interest, to evaluate their topological similarities. The proposed solution can be used via a user-friendly command line interface, also having a built-in guided mode (step-by-step) for defining input parameters.

RESULTS

We investigated the performance of DANTEml based on (i) performance evaluation on synthetic multilayer networks, (ii) statistical assessment of the resulting alignments, and (iii) alignment of real multilayer networks. DANTEml over performed a method that does not consider the distribution of nodes and edges over multiple layers by 1193.62%, and a method for temporal NA by 25.88%; we also performed the statistical assessment, which corroborates the significance of its own node mappings. In addition, we tested the proposed solution by using a real multilayer network in presence of several levels of noise, in accordance with the same outcome pursued for the NA on our dataset of synthetic networks. In this case, the improvement is even more evident: +4008.75% and +111.72%, compared to a method that does not consider the distribution of nodes and edges over multiple layers and a method for temporal NA, respectively.

CONCLUSIONS

DANTEml is a software tool for the PGNA of multilayer networks based on topological assessment, that is able to provide effective alignments both on synthetic and real multi layer networks, of which node mappings can be validated statistically. Our experimentation reported a high degree of reliability and effectiveness for the proposed solution.

scWECTA: A weighted ensemble classification framework for cell type assignment based on single cell transcriptome

Rapid advances in single-cell transcriptome analysis provide deeper insights into the study of tissue heterogeneity at the cellular level. Unsupervised clustering can identify potential cell populations in single-cell RNA-sequencing (scRNA-seq) data, but fail to further determine the identity of each cell. Existing automatic annotation methods using scRNA-seq data based on machine learning mainly use single feature set and single classifier. In view of this, we propose a Weighted Ensemble classification framework for Cell Type Annotation, named scWECTA, which improves the accuracy of cell type identification. scWECTA uses five informative gene sets and integrates five classifiers based on soft weighted ensemble framework. And the ensemble weights are inferred through the constrained non-negative least squares. Validated on multiple pairs of scRNA-seq datasets, scWECTA is able to accurately annotate scRNA-seq data across platforms and across tissues, especially for imbalanced data containing rare cell types. Moreover, scWECTA outperforms other comparable methods in balancing the prediction accuracy of common cell types and the unassigned rate of non-common cell types at the same time. The source code of scWECTA is freely available at https://github.com/ttren-sc/scWECTA.

Identifying Tumor-Associated Genes from Bilayer Networks of DNA Methylation Sites and RNAs

Network theory has attracted much attention from the biological community because of its high efficacy in identifying tumor-associated genes. However, most researchers have focused on single networks of single omics, which have less predictive power. With the available multiomics data, multilayer networks can now be used in molecular research. In this study, we achieved this with the construction of a bilayer network of DNA methylation sites and RNAs. We applied the network model to five types of tumor data to identify key genes associated with tumors. Compared with the single network, the proposed bilayer network resulted in more tumor-associated DNA methylation sites and genes, which we verified with prognostic and KEGG enrichment analyses.

Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context

At the heart of the cellular machinery through the regulation of cellular functions, protein-protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.