Detect the early-warning signals of diseases based on signaling pathway perturbations on a single sample.

BACKGROUND: During the pathogenesisof complex diseases, a sudden health deterioration will occur as results of the cumulative effect of various internal or external factors. The prediction of an early warning signal (pre-disease state) before such deterioration is very important in clinical practice, especially for a single sample. The single-sample landscape entropy (SLE) was proposed to tackle this issue. However, the PPI used in SLE was lack of definite biological meanings. Besides, the calculation of multiple correlations based on limited reference samples in SLE is time-consuming and suspect. RESULTS: Abnormal signals generally exert their effect through the static definite biological functions in signaling pathways across the development of diseases. Thus, it is a natural way to study the propagation of the early-warning signals based on the signaling pathways in the KEGG database. In this paper, we propose a signaling perturbation method named SSP, to study the early-warning signal in signaling pathways for single dynamic time-series data. Results in three real datasets including the influenza virus infection, lung adenocarcinoma, and acute lung injury show that the proposed SSP outperformed the SLE. Moreover, the early-warning signal can be detected by one important signaling pathway PI3K-Akt. CONCLUSIONS: These results all indicate that the static model in pathways could simplify the detection of the early-warning signals.

Predict lncRNA-drug associations based on graph neural network.

LncRNAs are an essential type of non-coding RNAs, which have been reported to be involved in various human pathological conditions. Increasing evidence suggests that drugs can regulate lncRNAs expression, which makes it possible to develop lncRNAs as therapeutic targets. Thus, developing in-silico methods to predict lncRNA-drug associations (LDAs) is a critical step for developing lncRNA-based therapies. In this study, we predict LDAs by using graph convolutional networks (GCN) and graph attention networks (GAT) based on lncRNA and drug similarity networks. Results show that our proposed method achieves good performance (average AUCs > 0.92) on five datasets. In addition, case studies and KEGG functional enrichment analysis further prove that the model can effectively identify novel LDAs. On the whole, this study provides a deep learning-based framework for predicting novel LDAs, which will accelerate the lncRNA-targeted drug development process.

Integrated edge information and pathway topology for drug-disease associations.

Drug repurposing is a promising approach to find new therapeutic indications for approved drugs. Many computational approaches have been proposed to prioritize candidate anticancer drugs by gene or pathway level. However, these methods neglect the changes in gene interactions at the edge level. To address the limitation, we develop a computational drug repurposing method (iEdgePathDDA) based on edge information and pathway topology. First, we identify drug-induced and disease-related edges (the changes in gene interactions) within pathways by using the Pearson correlation coefficient. Next, we calculate the inhibition score between drug-induced edges and disease-related edges. Finally, we prioritize drug candidates according to the inhibition score on all disease-related edges. Case studies show that our approach successfully identifies new drug-disease pairs based on CTD database. Compared to the state-of-the-art approaches, the results demonstrate our method has the superior performance in terms of five metrics across colorectal, breast, and lung cancer datasets.

Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers.

As a dynamical system, complex disease always has a sudden state transition at the tipping point, which is the result of the long-term accumulation of abnormal regulations. This paper proposes a novel approach to detect the early-warning signals of influenza A (H3N2 and H1N1) outbreaks by dysregulated dynamic network biomarkers (dysregulated DNBs) for individuals. The results of cross-validation show that our approach can detect early-warning signals before the symptom appears successfully. Unlike the traditional DNBs, our dysregulated DNBs are anchored and very few, which is essential for disease early diagnosis in clinical practice. Moreover, the genes of dysregulated DNBs are significantly enriched in the influenza-related pathways. The source code of this paper can be freely downloaded from https://github.com/YanhaoHuo/dysregulated-DNBs.git.

A drug repurposing method based on inhibition effect on gene regulatory network.

Numerous computational drug repurposing methods have emerged as efficient alternatives to costly and time-consuming traditional drug discovery approaches. Some of these methods are based on the assumption that the candidate drug should have a reversal effect on disease-associated genes. However, such methods are not applicable in the case that there is limited overlap between disease-related genes and drug-perturbed genes. In this study, we proposed a novel Drug Repurposing method based on the Inhibition Effect on gene regulatory network (DRIE) to identify potential drugs for cancer treatment. DRIE integrated gene expression profile and gene regulatory network to calculate inhibition score by using the shortest path in the disease-specific network. The results on eleven datasets indicated the superior performance of DRIE when compared to other state-of-the-art methods. Case studies showed that our method effectively discovered novel drug-disease associations. Our findings demonstrated that the top-ranked drug candidates had been already validated by CTD database. Additionally, it clearly identified potential agents for three cancers (colorectal, breast, and lung cancer), which was beneficial when annotating drug-disease relationships in the CTD. This study proposed a novel framework for drug repurposing, which would be helpful for drug discovery and development.

Analysis of Breast Cancer Based on the Dysregulated Network.

Breast cancer is a heterogeneous disease, and its development is closely associated with the underlying molecular regulatory network. In this paper, we propose a new way to measure the regulation strength between genes based on their expression values, and construct the dysregulated networks (DNs) for the four subtypes of breast cancer. Our results show that the key dysregulated networks (KDNs) are significantly enriched in critical breast cancer-related pathways and driver genes; closely related to drug targets; and have significant differences in survival analysis. Moreover, the key dysregulated genes could serve as potential driver genes, drug targets, and prognostic markers for each breast cancer subtype. Therefore, the KDN is expected to be an effective and novel way to understand the mechanisms of breast cancer.

PmiRtarbase: A positive miRNA-target regulations database.

MicroRNAs (miRNAs) are ~22 nt small non-coding RNA segments that are widely involved in the regulation of gene expression. Accumulating evidences show that miRNAs not only inhibit the expression of some targeted genes but also promote that of some targeted genes in specific conditions. Over the past decades, many miRNA-target databases have been developed from computational prediction and/or experimental validation perspectives. However, there is no database available to systematically collect positive miRNA-target associations that are essential in deciphering the miRNA regulation mechanism. To promote the miRNA study, we developed a new database: PmiRtarbase that acquires validated positive miRNA-target interactions by mining published literature. It includes 312 curated associations between 119 miRNAs and 169 genes in 8 species from 130 studies and summarizes the conditions and detailed descriptions of the miRNA-target associations. We also constructed a database named PmiRtarbase, a user-friendly interface to conveniently search and download all related entries. This elaborate database aims to serve as a beneficial resource for studying the miRNA positive regulation mechanism and miRNA-based therapeutics. DATA AVAILABILITY: The full positive miRNA-target data can be accessed through the link http://www.lwb-lab.cn/PmiRtarbase. Users of this dataset should acknowledge the contributions of the original authors and properly cite this article.

A simple pre-disease state prediction method based on variations of gene vector features.

BACKGROUND: The progression of disease can be divided into three states: normal, pre-disease, and disease. Since a pre-disease state is the tipping point of disease deterioration, accurately predicting pre-disease state may help to prevent the progression of disease and develop feasible treatment in time. METHODS: In the perspective of gene regulatory network, the expression of a gene is regulated by its upstream genes, and then it also regulates that of its downstream genes. In this study, we define the expression value of these genes as a gene vector to depict its state in a specific sample. Then, we propose a novel pre-disease prediction method by such vector features. RESULTS: The results of an influenza virus infection dataset show that our method can successfully predict the pre-disease state. Furthermore, the pre-disease state related genes predicted by our methods are highly associated with each other and enriched in influenza virus infection related pathways. In addition, our method is more time efficient in calculation than previous works. The code of our method is accessed at https://github.com/ZhenshenBao/sPGVF.git.

Identifying cancer specific signaling pathways based on the dysregulation between genes.

A large collection of studies has shown that the occurrence of cancer is related to the functional dysfunction of the pathways. Identification of cancer-related pathways could help researchers understand the mechanisms of complex diseases well. Whereas, most current signaling pathway analysis methods take no account of the gene interaction variations within pathways. Furthermore, considering that some pathways have connection with two or more cancer types, while some are likely to be cancer-type specific pathways. Identifying cancer-type specific pathways contributes to interpreting the different mechanisms of different cancer types. In this study, we first proposed a pathway analysis method named Pathway Analysis of Intergenic Regulation (PAIGR) to identify pathways with dysregulation between genes and compared the performance of this method with four existing methods on four colorectal cancer (CRC) datasets. The results showed that PAIGR could find cancer-related pathways more accurately. Moreover, in order to explore the relationship between the identified pathways and the cancer type, we constructed a pathway interaction network, in which nodes and edges represented pathways and interactions between pathways respectively. Highly connected pathways were considered to play a central role in an extensive range of biological processes, while sparsely connected pathways are considered to have certain specificity. Our results showed that pathways identified by PAIGR had a low nodal degree (i.e., a few numbers of interactions), which suggested that most of these pathways were cancer-type specific.

Identifying disease-associated signaling pathways through a novel effector gene analysis.

BACKGROUND: Signaling pathway analysis methods are commonly used to explain biological behaviors of disease cells. Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal signals they received. The signals that the effector genes receive can be quite different in normal vs. disease conditions. However, most of current signaling pathway analysis methods do not take these signal variations into consideration. METHODS: In this study, we developed a novel signaling pathway analysis method called signaling pathway functional attributes analysis (SPFA) method. This method analyzes the signal variations that effector genes received between two conditions (normal and disease) in different signaling pathways. RESULTS: We compared the SPFA method to seven other methods across 33 Gene Expression Omnibus datasets using three measurements: the median rank of target pathways, the median p-value of target pathways, and the percentages of significant pathways. The results confirmed that SPFA was the top-ranking method in terms of median rank of target pathways and the fourth best method in terms of median p-value of target pathways. SPFA's percentage of significant pathways was modest, indicating a good false positive rate and false negative rate. Overall, SPFA was comparable to the other methods. Our results also suggested that the signal variations calculated by SPFA could help identify abnormal functional attributes and parts of pathways. The SPFA R code and functions can be accessed at https://github.com/ZhenshenBao/SPFA.

Understanding the mechanisms of cancers based on function sub-pathways.

Pathway analysis has become a popular technology tool for gaining insight into the underlying biology of differentially expressed genes and proteins. Although many sub-pathways analysis methods have been proposed, the function of these sub-pathways is generally implicit. In this paper, we propose a function sub-pathway analysis (FSPA) method which includes all nodes reaching a specific function node at the downstream of pathways. The perturbation degree of a sub-pathway is defined as the negative of the log p-value of the sub-pathway. The proposed FSPA allows analyzing the differentially expressed genes in a sub-pathway with diseases in explicit function level. Results from six datasets of colorectal cancer, lung cancer and pancreatic cancer show that the proposed FSPA could identify more cancer associated pathways. And more importantly, it could identify which sub-pathways lead to a specific abnormal function, and to what extent it affects the function. Furthermore, the proposed perturbation degree could also analyze the imbalance of some functions involved in some biological process. The results by FSPA are helpful for elucidating the underlying mechanisms of cancers and designing therapeutic strategies.

Signalling pathway impact analysis based on the strength of interaction between genes.

Signalling pathway analysis is a popular approach that is used to identify significant cancer-related pathways based on differentially expressed genes (DEGs) from biological experiments. The main advantage of signalling pathway analysis lies in the fact that it assesses both the number of DEGs and the propagation of signal perturbation in signalling pathways. However, this method simplifies the interactions between genes by categorising them only as activation (+1) and suppression (-1), which does not encompass the range of interactions in real pathways, where interaction strength between genes may vary. In this study, the authors used newly developed signalling pathway impact analysis (SPIA) methods, SPIA based on Pearson correlation coefficient (PSPIA), and mutual information (MSPIA), to measure the interaction strength between pairs of genes. In analyses of a colorectal cancer dataset, a lung cancer dataset, and a pancreatic cancer dataset, PSPIA and MSPIA identified more candidate cancer-related pathways than were identified by SPIA. Generally, MSPIA performed better than PSPIA.