Multi-omics analyses provide novel biological insights to distinguish lobular ductal types of invasive breast cancers.

BACKGROUND: Invasive lobular carcinoma (ILC) treatment is similar to invasive ductal carcinoma (IDC; now invasive carcinoma-no special type, IBC-NST), based on its intrinsic subtype. However, further investigation is required for an integrative understanding of differentially perturbed molecular patterns and pathways in these histotypes. METHODS: A dataset of 780 IDC and 201 ILC samples from the TCGA-BRCA project for cross-platform multi-omics was analyzed. We leveraged a consensus approach integrating different bioinformatic algorithms to analyze mutations, CNAs, mRNA, miRNA abundance, methylation, and protein abundance to understand the complex crosstalks that distinguish ILC and IDC samples. A histotype-matched comparison was performed. We performed Cox survival analyses for prognosis based on our identified 53 histotype-specific and four discordant genes. RESULTS: Approximately 90% of ILC cases were of the luminal subtype. Somatic mutations in CDH1 were higher in ILC than in IDC (FDR-adjusted p < 0.01). Fifty-three significant oncogenic or tumor-suppressive DEGs were identified in a single histotype. PPAR signaling and lipolysis regulation in adipocytes were significantly enriched in ILC tumors. CDH1 protein had the highest differential abundance (AUC: 0.85). Moreover, BTG2, GSTA2, GPR37L1, and PGBD5 amplification was associated with poorer OS in ILC compared with no alteration. RIMS2, NACA4P, MYC, ZFPM2, and POU5F1B amplification showed a lower overall survival in patients with IDC. miR-195 showed an IDC-specific downregulation, causing overexpression of CCNE1. Integrative multi-omics supervised analysis identified 296 differentially expressed genes that successfully distinguished IDC and ILC histotypes. CONCLUSIONS: Our findings identify novel molecular candidates that potentially drive and modify the disease differentially among these histotypes.

A novel miRNA-based classification model of risks and stages for clear cell renal cell carcinoma patients.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal carcinoma and patients at advanced stage showed poor survival rate. Despite microRNAs (miRNAs) are used as potential biomarkers in many cancers, miRNA biomarkers for predicting the tumor stage of ccRCC are still limitedly identified. Therefore, we proposed a new integrated machine learning (ML) strategy to identify a novel miRNA signature related to tumor stage and prognosis of ccRCC patients using miRNA expression profiles. A multivariate Cox regression model with three hybrid penalties including Least absolute shrinkage and selection operator (Lasso), Adaptive lasso and Elastic net algorithms was used to screen relevant prognostic related miRNAs. The best subset regression (BSR) model was used to identify optimal prognostic model. Five ML algorithms were used to develop stage classification models. The biological significance of the miRNA signature was analyzed by utilizing DIANA-mirPath. RESULTS: A four-miRNA signature associated with survival was identified and the expression of this signature was strongly correlated with high risk patients. The high risk patients had unfavorable overall survival compared with the low risk group (HR = 4.523, P-value = 2.86e-08). Univariate and multivariate analyses confirmed independent and translational value of this predictive model. A combined ML algorithm identified six miRNA signatures for cancer staging prediction. After using the data balancing algorithm SMOTE, the Support Vector Machine (SVM) algorithm achieved the best classification performance (accuracy = 0.923, sensitivity = 0.927, specificity = 0.919, MCC = 0.843) when compared with other classifiers. Furthermore, enrichment analysis indicated that the identified miRNA signature involved in cancer-associated pathways. CONCLUSIONS: A novel miRNA classification model using the identified prognostic and tumor stage associated miRNA signature will be useful for risk and stage stratification for clinical practice, and the identified miRNA signature can provide promising insight to understand the progression mechanism of ccRCC.

Construction and Validation of a Prognostic Gene-Based Model for Overall Survival Prediction in Hepatocellular Carcinoma Using an Integrated Statistical and Bioinformatic Approach.

Hepatocellular carcinoma (HCC) is one of the most common lethal cancers worldwide and is often related to late diagnosis and poor survival outcome. More evidence is demonstrating that gene-based prognostic models can be used to predict high-risk HCC patients. Therefore, our study aimed to construct a novel prognostic model for predicting the prognosis of HCC patients. We used multivariate Cox regression model with three hybrid penalties approach including least absolute shrinkage and selection operator (Lasso), adaptive lasso and elastic net algorithms for informative prognostic-related genes selection. Then, the best subset regression was used to identify the best prognostic gene signature. The prognostic gene-based risk score was constructed using the Cox coefficient of the prognostic gene signature. The model was evaluated by Kaplan-Meier (KM) and receiver operating characteristic curve (ROC) analyses. A novel four-gene signature associated with prognosis was identified and the risk score was constructed based on the four-gene signature. The risk score efficiently distinguished the patients into a high-risk group with poor prognosis. The time-dependent ROC analysis revealed that the risk model had a good performance with an area under the curve (AUC) of 0.780, 0.732, 0.733 in 1-, 2- and 3-year prognosis prediction in The Cancer Genome Atlas (TCGA) dataset. Moreover, the risk score revealed a high diagnostic performance to classify HCC from normal samples. The prognosis and diagnosis prediction performances of risk scores were verified in external validation datasets. Functional enrichment analysis of the four-gene signature and its co-expressed genes involved in the metabolic and cell cycle pathways was constructed. Overall, we developed a novel-gene-based prognostic model to predict high-risk HCC patients and we hope that our findings can provide promising insight to explore the role of the four-gene signature in HCC patients and aid risk classification.

Physalin A attenuates inflammation through down-regulating c-Jun NH2 kinase phosphorylation/Activator Protein 1 activation and up-regulating the antioxidant activity.

Physalin A (PA), a withanolide, was isolated from Physalis angulata L. In this study, it is shown that PA can inhibit the production of inflammatory cytokines such as PGE2, NO, IL-1ß, IL-6, and TNF-α in LPS-induced RAW 264.7 cells. Furthermore, the results indicated that PA suppressed the IκB/NF-κB and JNK/ AP-1 inflammatory signaling pathways and inhibited the levels of pro-inflammatory factors iNOS and COX-2 in LPS-stimulated RAW 264.7 cells. In the carrageenan-induced mouse hind paw edema study, PA was shown to inhibit the production of inflammatory mediators such as NO, MDA, and TNF-α production. Conversely, the antioxidant factor levels of SOD, CAT, and GPx were all increased by the treated PA. According to the data, we are suggesting that the anti-inflammatory effects of PA may be through the suppressions of the JNK/AP-1 and IκB/NF-κB signaling pathways and up-regulation of the anti-oxidative activity.

Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory.

BACKGROUND: Non-small cell lung cancer (NSCLC) is one of the leading causes of death globally, and research into NSCLC has been accumulating steadily over several years. Drug repositioning is the current trend in the pharmaceutical industry for identifying potential new uses for existing drugs and accelerating the development process of drugs, as well as reducing side effects. RESULTS: This work integrates two approaches--machine learning algorithms and topological parameter-based classification--to develop a novel pipeline of drug repositioning to analyze four lung cancer microarray datasets, enriched biological processes, potential therapeutic drugs and targeted genes for NSCLC treatments. A total of 7 (8) and 11 (12) promising drugs (targeted genes) were discovered for treating early- and late-stage NSCLC, respectively. The effectiveness of these drugs is supported by the literature, experimentally determined in-vitro IC50 and clinical trials. This work provides better drug prediction accuracy than competitive research according to IC50 measurements. CONCLUSIONS: With the novel pipeline of drug repositioning, the discovery of enriched pathways and potential drugs related to NSCLC can provide insight into the key regulators of tumorigenesis and the treatment of NSCLC. Based on the verified effectiveness of the targeted drugs predicted by this pipeline, we suggest that our drug-finding pipeline is effective for repositioning drugs.

Disturbance of Arabidopsis thaliana microRNA-regulated pathways by Xcc bacterial effector proteins.

Plants are continuously subjected to infection by pathogens, including bacteria and viruses. Bacteria can inject a variety of effector proteins into the host to reprogram host defense mechanism. It is known that microRNAs participate in plant disease resistance to bacterial pathogens and previous studies have suggested that some bacterial effectors have evolved to disturb the host's microRNA-regulated pathways; and so enabling infection. In this study, the inter-species interaction between an Xanthomonas campestris pv campestris (Xcc) pathogen effector and Arabidopsis thaliana microRNA transcription promoter was investigated using three methods: (1) interolog, (2) alignment based on using transcription factor binding site profile matrix, and (3) the web-based binding site prediction tool, PATSER. Furthermore, we integrated another two data sets from our previous study into the present web-based system. These are (1) microRNA target genes and their downstream effects mediated by protein-protein interaction (PPI), and (2) the Xcc-Arabidopsis PPI information. This present work is probably the first comprehensive study of constructing pathways that comprises effector, microRNA, target genes and PPI for the study of pathogen-host interactions. It is expected that this study may help to elucidate the role of pathogen-host interplay in a plant's immune system. The database is freely accessible at: http://ppi.bioinfo.asia.edu.tw/EDMRP .

Toll-like receptor 9 SNPs are susceptible to the development and progression of membranous glomerulonephritis: 27 years follow-up in Taiwan.

The purpose of this study was to determine whether toll-like receptors 9 (TLR9) gene polymorphisms (rs352139 and rs352140) were markers of susceptibility to the development and progression of membranous nephropathy (MGN) in Taiwanese patients. The polymorphisms were investigated by polymerase chain reaction in 397 Taiwanese individuals (134 MGN patients and 263 controls). Patients with malignancy, chronic infectious diseases, lupus nephritis, or drug-induced secondary MGN were excluded from the study. Data showed AA genotype at rs352139 SNP or GG genotype at rs352140 SNP may indicate higher risk for MGN (odds ratio [OR] = 1.55; 95% confidence interval [CI] = 1.02-2.35, at rs352139 SNP; OR = 1.57; 95% CI = 1.03-2.39, at rs352140 SNP). However, MGN patients with A-G haplotype were susceptible for decreased creatinine clearance rate and for seriously tubule-interstitial fibrosis. The result suggests for the first time that TLR9 (rs352139 and rs352140) polymorphisms may contribute to the development and progression of MGN.

Cluster-based text mining for extracting drug candidates for the prevention of COVID-19 from the biomedical literature.

Objective: The coronavirus disease 2019 (COVID-19) health crisis that began at the end of 2019 made researchers around the world quickly race to find effective solutions. Related literature exploded and it was inevitable that an automated approach was needed to find useful information, namely text mining, to overcome COVID-19, especially in terms of drug candidate discovery. While text mining methods for finding drug candidates mostly try to extract bioentity associations from PubMed, very few of them mine with a clustering approach. The purpose of this study was to demonstrate the effectiveness of our approach to identify drugs for the prevention of COVID-19 through literature review, cluster analysis, drug docking calculations, and clinical trial data. Methods: This research was conducted in four main stages. First, the text mining stage was carried out by involving Bidirectional Encoder Representations from Transformers for Biomedical to obtain vector representation of each word in the sentence from texts. The next stage generated the disease-drug associations, which were obtained from the correlation between disease and drug. Next, the clustering stage grouped the rules through the similarity of diseases by utilizing Term Frequency-Inverse Document Frequency as its feature. Finally, the drug candidate extraction stage was processed through leveraging PubChem and DrugBank databases. We further used the drug docking package AUTODOCK VINA in PyRx software to verify the results. Results: Comparative analyses showed that the percentage of findings using mining with clustering outperformed mining without clustering in all experimental settings. In addition, we suggest that the top three drugs/phytochemicals by drug docking analysis may be effective in preventing COVID-19. Conclusions: The proposed method for text mining utilizing the clustering method is quite promising in the discovery of drug candidates for the prevention of COVID-19 through the biomedical literature.

A database of integrated molecular and phytochemical interactions of the foxm1 pathway for lung cancer.

The FoxM1 pathway is an oncogenic signaling pathway involved in essential mechanisms including control cell-cycle progression, apoptosis and cell growth which are the common hallmarks of various cancers. Although its biological functions in the tumor development and progression are known, the mechanism by which it participates in those processes is not understood. The present work reveals images of the oncogenic FoxM1 pathway controlling the cell cycle process with alternative treatment options via phytochemical substances in the lung cancer study. The downstream significant protein modules of the FoxM1 pathway were extracted by the Molecular Complex Detection (MCODE) and the maximal clique (Mclique) algorithms. Furthermore, the effects of post-transcriptional modification by microRNA, transcription factor binding and the phytochemical compounds are observed through their interactions with the lung cancer protein modules. We provided two case studies to demonstrate the usefulness of our database. Our results suggested that the combination of various phytochemicals is effective in the treatment of lung cancer. The ultimate goal of the present work is to partly support the discovery of plant-derived compounds in combination treatment of classical chemotherapeutic agents to increase the efficacy of lung cancer method probably with minor side effects. Furthermore, a web-based system displaying results of the present work is set up for investigators posing queries at http://sit.mfu.ac.th/lcgdb/index_FoxM1.php.Communicated by Ramaswamy H. Sarma.

Network subgraph-based approach for analyzing and comparing molecular networks.

Molecular networks are built up from genetic elements that exhibit feedback interactions. Here, we studied the problem of measuring the similarity of directed networks by proposing a novel alignment-free approach: the network subgraph-based approach. Our approach does not make use of randomized networks to determine modular patterns embedded in a network, and this method differs from the network motif and graphlet methods. Network similarity was quantified by gauging the difference between the subgraph frequency distributions of two networks using Jensen-Shannon entropy. We applied the subgraph approach to study three types of molecular networks, i.e., cancer networks, signal transduction networks, and cellular process networks, which exhibit diverse molecular functions. We compared the performance of our subgraph detection algorithm with other algorithms, and the results were consistent, but other algorithms could not address the issue of subgraphs/motifs embedded within a subgraph/motif. To evaluate the effectiveness of the subgraph-based method, we applied the method along with the Jensen-Shannon entropy to classify six network models, and it achieves a 100% accuracy of classification. The proposed information-theoretic approach allows us to determine the structural similarity of two networks regardless of node identity and network size. We demonstrated the effectiveness of the subgraph approach to cluster molecular networks that exhibit similar regulatory interaction topologies. As an illustration, our method can identify (i) common subgraph-mediated signal transduction and/or cellular processes in AML and pancreatic cancer, and (ii) scaffold proteins in gastric cancer and hepatocellular carcinoma; thus, the results suggested that there are common regulation modules for cancer formation. We also found that the underlying substructures of the molecular networks are dominated by irreducible subgraphs; this feature is valid for the three classes of molecular networks we studied. The subgraph-based approach provides a systematic scenario for analyzing, compare and classifying molecular networks with diverse functionalities.

ncRNAppi--a tool for identifying disease-related miRNA and siRNA targeting pathways.

UNLABELLED: Currently, there are a number of databases which store microRNA (miRNA) information, and tools available which provide miRNA target prediction. In this article, we describe a novel web-based tool that integrate the miRNA-targeted mRNA data, protein-protein interactions (PPI) records, tissues, biochemical pathways, human disease and gene function information to establish a disease-related miRNA target pathway database. This database is unique in the sense that it links miRNA target genes with their PPI partners according to being tissue- and diseases-specific or both. The same approach is also applied to siRNA data. This database provides two types of searches: (i) tissue- and (ii) disease-specific miRNA (or siRNA) targeting pathways. The search allows one to identify tissue- or disease-specific miRNA (or siRNA) target gene's PPI partners two levels beyond. AVAILABILITY: The release version 1.0 is a freely accessible database available at http://ncrnappi.cs.nthu.edu.tw and http://ncRNAppi.bioinfo.asia.edu.tw/.

Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method.

Cancer is a highly complex disease caused by multiple genetic factors. MicroRNA (miRNA) and mRNA expression profiles are useful for identifying prognostic biomarkers for cancer. Kidney renal clear cell carcinoma (KIRC), which accounts for more than 70% of all renal malignant tumour cases, was selected for our analysis. Traditional methods of identifying cancer prognostic markers may not be accurate. Tensor decomposition (TD) is a useful method uncovering the underlying low-dimensional structures in the tensor. The TD-based unsupervised feature extraction method was applied to analyse mRNA and miRNA expression profiles. Biological annotations of the prognostic miRNAs and mRNAs were examined utilizing the pathway and oncogenic signature databases DIANA-miRPath and MSigDB. TD identified the miRNA signatures and the associated genes. These genes were found to be involved in cancer-related pathways, and 23 genes were significantly correlated with the survival of KIRC patients. We demonstrated that the results are robust and not highly dependent upon the databases we selected. Compared with traditional supervised methods tested, TD achieves much better performance in selecting prognostic miRNAs and mRNAs. These results suggest that integrated analysis using the TD-based unsupervised feature extraction technique is an effective strategy for identifying prognostic signatures in cancer studies.

Dissecting molecular network structures using a network subgraph approach.

Biological processes are based on molecular networks, which exhibit biological functions through interactions of genetic elements or proteins. This study presents a graph-based method to characterize molecular networks by decomposing the networks into directed multigraphs: network subgraphs. Spectral graph theory, reciprocity and complexity measures were used to quantify the network subgraphs. Graph energy, reciprocity and cyclomatic complexity can optimally specify network subgraphs with some degree of degeneracy. Seventy-one molecular networks were analyzed from three network types: cancer networks, signal transduction networks, and cellular processes. Molecular networks are built from a finite number of subgraph patterns and subgraphs with large graph energies are not present, which implies a graph energy cutoff. In addition, certain subgraph patterns are absent from the three network types. Thus, the Shannon entropy of the subgraph frequency distribution is not maximal. Furthermore, frequently-observed subgraphs are irreducible graphs. These novel findings warrant further investigation and may lead to important applications. Finally, we observed that cancer-related cellular processes are enriched with subgraph-associated driver genes. Our study provides a systematic approach for dissecting biological networks and supports the conclusion that there are organizational principles underlying molecular networks.

Autonomy-Supportive Teaching and Basic Psychological Need Satisfaction among School Students: The Role of Mindfulness.

Grounded in self-determination theory, the purpose of this study was to investigate the relationships between autonomy-supportive teaching, mindfulness, and basic psychological need satisfaction/frustration. Secondary school students (n = 390, Mage = 15) responded to a survey form measuring psychological constructs pertaining to the research purpose. A series of multiple regression analysis showed that autonomy-supportive teaching and mindfulness positively predicted need satisfaction and negatively predicted need frustration. In addition, the associations between autonomy-supportive teaching and need satisfaction/frustration were moderated by mindfulness. Students higher in mindfulness were more likely to feel need satisfaction and less likely to experience need frustration, even in a low autonomy-supportive teaching environment. These results speak to the relevance of creating autonomy-supportive teaching environments and highlight mindfulness as a potential pathway to basic psychological need satisfaction in educational settings.

Applications of domain-domain interactions in pathway study.

The domain combination pair approach is employed to derive putative protein domain-domain interactions (DDI) from the protein-protein interactions (PPI) database DIP. The results of putative DDI are computed for seven species. To determine the prediction performance, putative DDI results are compared with that of the database InterDom, where an average matching ratio of about 76% can be achieved. Several real PPI pathways are reconstructed based on the predicted DDI results. It is found that the pathways could be reconstructed with reasonable accuracy. Furthermore, a novel quantity, so called AP-order index, is introduced to predict the regulatory order for six PPI pathways. It is found that the AP-order index is a very reliable parameter to determine the regulatory order of PPI.

Drug repurposing and therapeutic anti-microRNA predictions for inhibition of oxidized low-density lipoprotein-induced vascular smooth muscle cell-associated diseases.

Drug repurposing is a new method for disease treatments, which accelerates the identification of new uses for existing drugs with minimal side effects for patients. MicroRNA-based therapeutics are a class of drugs that have been used in gene therapy following the FDA's approval of the first anti-sense therapy. This study examines the effects of oxLDL on vascular smooth muscle cells (VSMCs) and identifies potential drugs and antimiRs for treating VSMC-associated diseases. The Connectivity Map (cMap) database is utilized to identify potential new uses of existing drugs. The success of the identifications was supported by MTT assay, clonogenic assay and clinical trial data. Specifically, 37 drugs, some of which are undergoing clinical trials, were identified. Three of the identified drugs exhibit IC50 activities. Among the 37 drugs' targets, three differentially expressed genes (DEGs) are identified as drug targets by using both the DrugBank and the NCBI PubChem Compound databases. Also, one DEG, DNMT1, which is regulated by 17 miRNAs, where these miRNAs are potential targets for developing antimiR-based miRNA therapy, is found.

Graph theory and stability analysis of protein complex interaction networks.

Protein complexes play an essential role in many biological processes. Complexes can interact with other complexes to form protein complex interaction network (PCIN) that involves in important cellular processes. There are relatively few studies on examining the interaction topology among protein complexes; and little is known about the stability of PCIN under perturbations. We employed graph theoretical approach to reveal hidden properties and features of four species PCINs. Two main issues are addressed, (i) the global and local network topological properties, and (ii) the stability of the networks under 12 types of perturbations. According to the topological parameter classification, we identified some critical protein complexes and validated that the topological analysis approach could provide meaningful biological interpretations of the protein complex systems. Through the Kolmogorov-Smimov test, we showed that local topological parameters are good indicators to characterise the structure of PCINs. We further demonstrated the effectiveness of the current approach by performing the scalability and data normalization tests. To measure the robustness of PCINs, we proposed to consider eight topological-based perturbations, which are specifically applicable in scenarios of targeted, sustained attacks. We found that the degree-based, betweenness-based and brokering-coefficient-based perturbations have the largest effect on network stability.

Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells.

BACKGROUND: Abnormal proliferation of vascular smooth muscle cells (VSMC) is a major cause of cardiovascular diseases (CVDs). Many studies suggest that vascular injury triggers VSMC dedifferentiation, which results in VSMC changes from a contractile to a synthetic phenotype; however, the underlying molecular mechanisms are still unclear. METHODS: In this study, we examined how VSMC responds under mechanical stress by using time-course microarray data. A three-phase study was proposed to investigate the stress-induced differentially expressed genes (DEGs) in VSMC. First, DEGs were identified by using the moderated t-statistics test. Second, more DEGs were inferred by using the Gaussian Graphical Model (GGM). Finally, the topological parameters-based method and cluster analysis approach were employed to predict the last batch of DEGs. To identify the potential drugs for vascular diseases involve VSMC proliferation, the drug-gene interaction database, Connectivity Map (cMap) was employed. Success of the predictions were determined using in-vitro data, i.e. MTT and clonogenic assay. RESULTS: Based on the differential expression calculation, at least 23 DEGs were found, and the findings were qualified by previous studies on VSMC. The results of gene set enrichment analysis indicated that the most often found enriched biological processes are cell-cycle-related processes. Furthermore, more stress-induced genes, well supported by literature, were found by applying graph theory to the gene association network (GAN). Finally, we showed that by processing the cMap input queries with a cluster algorithm, we achieved a substantial increase in the number of potential drugs with experimental IC50 measurements. With this novel approach, we have not only successfully identified the DEGs, but also improved the DEGs prediction by performing the topological and cluster analysis. Moreover, the findings are remarkably validated and in line with the literature. Furthermore, the cMap and DrugBank resources were used to identify potential drugs and targeted genes for vascular diseases involve VSMC proliferation. Our findings are supported by in-vitro experimental IC50, binding activity data and clinical trials. CONCLUSION: This study provides a systematic strategy to discover potential drugs and target genes, by which we hope to shed light on the treatments of VSMC proliferation associated diseases.

DNA methylation-regulated microRNA pathways in ovarian serous cystadenocarcinoma: A meta-analysis.

Epigenetic regulation has been linked to the initiation and progression of cancer. Aberrant expression of microRNAs (miRNAs) is one such mechanism that can activate or silence oncogenes (OCGs) and tumor suppressor genes (TSGs) in cells. A growing number of studies suggest that miRNA expression can be regulated by methylation modification, thus triggering cancer development. However, there is no comprehensive in silico study concerning miRNA regulation by direct DNA methylation in cancer. Ovarian serous cystadenocarcinoma (OSC) was therefore chosen as a tumor model for the present work. Twelve batches of OSC data, with at least 35 patient samples in each batch, were obtained from The Cancer Genome Atlas (TCGA) database. The Spearman rank correlation coefficient (SRCC) was used to quantify the correlation between the CpG DNA methylation level and miRNA expression level. Meta-analysis was performed to reduce the effects of biological heterogeneity among different batches. MiRNA-target interactions were also inferred by computing SRCC and meta-analysis to assess the correlation between miRNA expression and cancer-associated gene expression and the interactions were further validated by a query against the miRTarBase database. A total of 26 potential epigenetic-regulated miRNA genes that can target OCGs or TSGs in OSC were found to show biological relevance between DNA methylation and miRNA gene expression. Furthermore, some of the identified DNA-methylated miRNA genes; for instance, the miR-200 family, were previously identified as epigenetic-regulated miRNAs and correlated with poor survival of ovarian cancer. We also found that several miRNA target genes, BTG3, NDN, HTRA3, CDC25A, and HMGA2 were also related to the poor outcomes in ovarian cancer. The present study proposed a systematic strategy to construct highly confident epigenetic-regulated miRNA pathways for OSC. The findings are validated and are in line with the literature. The inclusion of direct DNA methylated miRNA events may offer another layer of explanation that along with genetics can give a better understanding of the carcinogenesis process.

Prediction of cancer proteins by integrating protein interaction, domain frequency, and domain interaction data using machine learning algorithms.

Many proteins are known to be associated with cancer diseases. It is quite often that their precise functional role in disease pathogenesis remains unclear. A strategy to gain a better understanding of the function of these proteins is to make use of a combination of different aspects of proteomics data types. In this study, we extended Aragues's method by employing the protein-protein interaction (PPI) data, domain-domain interaction (DDI) data, weighted domain frequency score (DFS), and cancer linker degree (CLD) data to predict cancer proteins. Performances were benchmarked based on three kinds of experiments as follows: (I) using individual algorithm, (II) combining algorithms, and (III) combining the same classification types of algorithms. When compared with Aragues's method, our proposed methods, that is, machine learning algorithm and voting with the majority, are significantly superior in all seven performance measures. We demonstrated the accuracy of the proposed method on two independent datasets. The best algorithm can achieve a hit ratio of 89.4% and 72.8% for lung cancer dataset and lung cancer microarray study, respectively. It is anticipated that the current research could help understand disease mechanisms and diagnosis.