iGluK-Deep: computational identification of lysine glutarylation sites using deep neural networks with general pseudo amino acid compositions

An MCDM approach for Reverse vaccinology model to predict bacterial protective antigens

Reverse vaccinology (RV) is a significant step in sensible vaccine design. In recent years, many machine learning (ML) methods have been used to improve RV prediction accuracy. However, there are still issues with prediction accuracy and programme accessibility in ML-based RV. This paper presents a supervised ML-based method to classify bacterial protective antigens (BPAgs) and identify the model(s) that consistently perform well for the training dataset. Six ML classifiers are used for testing with physiochemical features extracted from a comprehensive training dataset. Selecting the best performing model from different performance metrics (accuracy, precision, recall, F1-score, and AUC-ROC) has not been easy, because all the metrics has the same importance to predict BPAgs. To fix this issue, we propose a soft and hard ranking model based on multi-criteria decision-making (MCDM) approach for selecting the best performing ML method that classifies BPAgs. First, our proposed model uses homologous proteins (positive and negative samples) from Protegen and Uniprot databases. Second, we applied four strategies of Synthetic Minority Oversampling Technique and Edited Nearest Neighbour (SMOTE-ENN) to handle the data imbalance problem and train the model using ML methods. Third, we consider MCDM-based technique for order preference by similarity to the ideal solution (TOPSIS) method integrated with soft and hard ranking model. The entropy is used to obtain weighted evaluation criteria for ranking the models. Our experimental evaluations show that the proposed method with best performing models (Random Forest and Extreme Gradient Boosting) outperforms compared to existing open-source RV methods using benchmark datasets.

m1A-Ensem: accurate identification of 1-methyladenosine sites through ensemble models

BACKGROUND

1-methyladenosine (m1A) is a variant of methyladenosine that holds a methyl substituent in the 1st position having a prominent role in RNA stability and human metabolites.

OBJECTIVE

Traditional approaches, such as mass spectrometry and site-directed mutagenesis, proved to be time-consuming and complicated.

METHODOLOGY

The present research focused on the identification of m1A sites within RNA sequences using novel feature development mechanisms. The obtained features were used to train the ensemble models, including blending, boosting, and bagging. Independent testing and k-fold cross validation were then performed on the trained ensemble models.

RESULTS

The proposed model outperformed the preexisting predictors and revealed optimized scores based on major accuracy metrics.

CONCLUSION

For research purpose, a user-friendly webserver of the proposed model can be accessed through https://taseersuleman-m1a-ensem1.streamlit.app/ .

From G1 to M: a comparative study of methods for identifying cell cycle phases

Accurate identification of cell cycle phases in single-cell RNA-sequencing (scRNA-seq) data is crucial for biomedical research. Many methods have been developed to tackle this challenge, employing diverse approaches to predict cell cycle phases. In this review article, we delve into the standard processes in identifying cell cycle phases within scRNA-seq data and present several representative methods for comparison. To rigorously assess the accuracy of these methods, we propose an error function and employ multiple benchmarking datasets encompassing human and mouse data. Our evaluation results reveal a key finding: the fit between the reference data and the dataset being analyzed profoundly impacts the effectiveness of cell cycle phase identification methods. Therefore, researchers must carefully consider the compatibility between the reference data and their dataset to achieve optimal results. Furthermore, we explore the potential benefits of incorporating benchmarking data with multiple known cell cycle phases into the analysis. Merging such data with the target dataset shows promise in enhancing prediction accuracy. By shedding light on the accuracy and performance of cell cycle phase prediction methods across diverse datasets, this review aims to motivate and guide future methodological advancements. Our findings offer valuable insights for researchers seeking to improve their understanding of cellular dynamics through scRNA-seq analysis, ultimately fostering the development of more robust and widely applicable cell cycle identification methods.

GBDT_KgluSite: An improved computational prediction model for lysine glutarylation sites based on feature fusion and GBDT classifier

BACKGROUND

Lysine glutarylation (Kglu) is one of the most important Post-translational modifications (PTMs), which plays significant roles in various cellular functions, including metabolism, mitochondrial processes, and translation. Therefore, accurate identification of the Kglu site is important for elucidating protein molecular function. Due to the time-consuming and expensive limitations of traditional biological experiments, computational-based Kglu site prediction research is gaining more and more attention.

RESULTS

In this paper, we proposed GBDT_KgluSite, a novel Kglu site prediction model based on GBDT and appropriate feature combinations, which achieved satisfactory performance. Specifically, seven features including sequence-based features, physicochemical property-based features, structural-based features, and evolutionary-derived features were used to characterize proteins. NearMiss-3 and Elastic Net were applied to address data imbalance and feature redundancy issues, respectively. The experimental results show that GBDT_KgluSite has good robustness and generalization ability, with accuracy and AUC values of 93.73%, and 98.14% on five-fold cross-validation as well as 90.11%, and 96.75% on the independent test dataset, respectively.

CONCLUSION

GBDT_KgluSite is an effective computational method for identifying Kglu sites in protein sequences. It has good stability and generalization ability and could be useful for the identification of new Kglu sites in the future. The relevant code and dataset are available at https://github.com/flyinsky6/GBDT_KgluSite .

The role of ncRNA regulatory mechanisms in diseases-case on gestational diabetes

Non-coding RNAs (ncRNAs) are a class of RNA molecules that do not have the potential to encode proteins. Meanwhile, they can occupy a significant portion of the human genome and participate in gene expression regulation through various mechanisms. Gestational diabetes mellitus (GDM) is a pathologic condition of carbohydrate intolerance that begins or is first detected during pregnancy, making it one of the most common pregnancy complications. Although the exact pathogenesis of GDM remains unclear, several recent studies have shown that ncRNAs play a crucial regulatory role in GDM. Herein, we present a comprehensive review on the multiple mechanisms of ncRNAs in GDM along with their potential role as biomarkers. In addition, we investigate the contribution of deep learning-based models in discovering disease-specific ncRNA biomarkers and elucidate the underlying mechanisms of ncRNA. This might assist community-wide efforts to obtain insights into the regulatory mechanisms of ncRNAs in disease and guide a novel approach for early diagnosis and treatment of disease.

A Framework for Prediction of Oncogenomic Progression Aiding Personalized Treatment of Gastric Cancer

Mutations in genes can alter their DNA patterns, and by recognizing these mutations, many carcinomas can be diagnosed in the progression stages. The human body contains many hidden and enigmatic features that humankind has not yet fully understood. A total of 7539 neoplasm cases were reported from 1 January 2021 to 31 December 2021. Of these, 3156 were seen in males (41.9%) and 4383 (58.1%) in female patients. Several machine learning and deep learning frameworks are already implemented to detect mutations, but these techniques lack generalized datasets and need to be optimized for better results. Deep learning-based neural networks provide the computational power to calculate the complex structures of gastric carcinoma-driven gene mutations. This study proposes deep learning approaches such as long and short-term memory, gated recurrent units and bi-LSTM to help in identifying the progression of gastric carcinoma in an optimized manner. This study includes 61 carcinogenic driver genes whose mutations can cause gastric cancer. The mutation information was downloaded from intOGen.org and normal gene sequences were downloaded from asia.ensembl.org, as explained in the data collection section. The proposed deep learning models are validated using the self-consistency test (SCT), 10-fold cross-validation test (FCVT), and independent set test (IST); the IST prediction metrics of accuracy, sensitivity, specificity, MCC and AUC of LSTM, Bi-LSTM, and GRU are 97.18%, 98.35%, 96.01%, 0.94, 0.98; 99.46%, 98.93%, 100%, 0.989, 1.00; 99.46%, 98.93%, 100%, 0.989 and 1.00, respectively.

Ensemble Learning for Hormone Binding Protein Prediction: A Promising Approach for Early Diagnosis of Thyroid Hormone Disorders in Serum

Hormone-binding proteins (HBPs) are specific carrier proteins that bind to a given hormone. A soluble carrier hormone binding protein (HBP), which can interact non-covalently and specifically with growth hormone, modulates or inhibits hormone signaling. HBP is essential for the growth of life, despite still being poorly understood. Several diseases, according to some data, are caused by HBPs that express themselves abnormally. Accurate identification of these molecules is the first step in investigating the roles of HBPs and understanding their biological mechanisms. For a better understanding of cell development and cellular mechanisms, accurate HBP determination from a given protein sequence is essential. Using traditional biochemical experiments, it is difficult to correctly separate HBPs from an increasing number of proteins because of the high experimental costs and lengthy experiment periods. The abundance of protein sequence data that has been gathered in the post-genomic era necessitates a computational method that is automated and enables quick and accurate identification of putative HBPs within a large number of candidate proteins. A brand-new machine-learning-based predictor is suggested as the HBP identification method. To produce the desirable feature set for the method proposed, statistical moment-based features and amino acids were combined, and the random forest was used to train the feature set. During 5-fold cross validation experiments, the suggested method achieved 94.37% accuracy and 0.9438 F1-scores, respectively, demonstrating the importance of the Hahn moment-based features.

Computational identification of promoters in Klebsiella aerogenes by using support vector machine

Promoters are the basic functional cis-elements to which RNA polymerase binds to initiate the process of gene transcription. Comprehensive understanding gene expression and regulation depends on the precise identification of promoters, as they are the most important component of gene expression. This study aimed to develop a machine learning-based model to predict promoters in Klebsiella aerogenes (K. aerogenes). In the prediction model, the promoter sequences in K. aerogenes genome were encoded by pseudo k-tuple nucleotide composition (PseKNC) and position-correlation scoring function (PCSF). Numerical features were obtained and then optimized using mRMR by combining with support vector machine (SVM) and 5-fold cross-validation (CV). Subsequently, these optimized features were inputted into SVM-based classifier to discriminate promoter sequences from non-promoter sequences in K. aerogenes. Results of 10-fold CV showed that the model could yield the overall accuracy of 96.0% and the area under the ROC curve (AUC) of 0.990. We hope that this model will provide help for the study of promoter and gene regulation in K. aerogenes.

DeepDN_iGlu: prediction of lysine glutarylation sites based on attention residual learning method and DenseNet

As a key issue in orchestrating various biological processes and functions, protein post-translational modification (PTM) occurs widely in the mechanism of protein's function of animals and plants. Glutarylation is a type of protein-translational modification that occurs at active ε-amino groups of specific lysine residues in proteins, which is associated with various human diseases, including diabetes, cancer, and glutaric aciduria type I. Therefore, the issue of prediction for glutarylation sites is particularly important. This study developed a brand-new deep learning-based prediction model for glutarylation sites named DeepDN_iGlu via adopting attention residual learning method and DenseNet. The focal loss function is utilized in this study in place of the traditional cross-entropy loss function to address the issue of a substantial imbalance in the number of positive and negative samples. It can be noted that DeepDN_iGlu based on the deep learning model offers a greater potential for the glutarylation site prediction after employing the straightforward one hot encoding method, with Sensitivity (Sn), Specificity (Sp), Accuracy (ACC), Mathews Correlation Coefficient (MCC), and Area Under Curve (AUC) of 89.29%, 61.97%, 65.15%, 0.33 and 0.80 accordingly on the independent test set. To the best of the authors' knowledge, this is the first time that DenseNet has been used for the prediction of glutarylation sites. DeepDN_iGlu has been deployed as a web server (https://bioinfo.wugenqiang.top/~smw/DeepDN_iGlu/) that is available to make glutarylation site prediction data more accessible.

iDHU-Ensem: Identification of dihydrouridine sites through ensemble learning models

Background

Dihydrouridine (D) is one of the most significant uridine modifications that have a prominent occurrence in eukaryotes. The folding and conformational flexibility of transfer RNA (tRNA) can be attained through this modification.

Objective

The modification also triggers lung cancer in humans. The identification of D sites was carried out through conventional laboratory methods; however, those were costly and time-consuming. The readiness of RNA sequences helps in the identification of D sites through computationally intelligent models. However, the most challenging part is turning these biological sequences into distinct vectors.

Methods

The current research proposed novel feature extraction mechanisms and the identification of D sites in tRNA sequences using ensemble models. The ensemble models were then subjected to evaluation using k-fold cross-validation and independent testing.

Results

The results revealed that the stacking ensemble model outperformed all the ensemble models by revealing 0.98 accuracy, 0.98 specificity, 0.97 sensitivity, and 0.92 Matthews Correlation Coefficient. The proposed model, iDHU-Ensem, was also compared with pre-existing predictors using an independent test. The accuracy scores have shown that the proposed model in this research study performed better than the available predictors.

Conclusion

The current research contributed towards the enhancement of D site identification capabilities through computationally intelligent methods. A web-based server, iDHU-Ensem, was also made available for the researchers at https://taseersuleman-idhu-ensem-idhu-ensem.streamlit.app/.

m1A-pred: Prediction of Modified 1-methyladenosine Sites in RNA Sequences through Artificial Intelligence

BACKGROUND

The process of nucleotides modification or methyl groups addition to nucleotides is known as post-transcriptional modification (PTM). 1-methyladenosine (m1A) is a type of PTM formed by adding a methyl group to the nitrogen at the 1st position of the adenosine base. Many human disorders are associated with m1A, which is widely found in ribosomal RNA and transfer RNA.

OBJECTIVE

The conventional methods such as mass spectrometry and site-directed mutagenesis proved to be laborious and burdensome. Systematic identification of modified sites from RNA sequences is gaining much attention nowadays. Consequently, an extreme gradient boost predictor, m1A-Pred, is developed in this study for the prediction of modified m1A sites.

METHODS

The current study involves the extraction of position and composition-based properties within nucleotide sequences. The extraction of features helps in the development of the features vector. Statistical moments were endorsed for dimensionality reduction in the obtained features.

RESULTS

Through a series of experiments using different computational models and evaluation methods, it was revealed that the proposed predictor, m1A-pred, proved to be the most robust and accurate model for the identification of modified sites.

AVAILABILITY AND IMPLEMENTATION

To enhance the research on m¹A sites, a friendly server was also developed, which was the final phase of this research.

FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites

Glutarylation is a post-translational modification which plays an irreplaceable role in various functions of the cell. Therefore, it is very important to accurately identify the glutarylation substrates and its corresponding glutarylation sites. In recent years, many computational methods of glutarylation sites have emerged one after another, but there are still many limitations, among which noisy data and the class imbalance problem caused by the uncertainty of non-glutarylation sites are great challenges. In this study, we propose a new semi-supervised learning algorithm, named FCCCSR, to identify reliable non-glutarylation lysine sites from unlabeled samples as negative samples. FCCCSR first finds core objects from positive samples according to reverse nearest neighbor information, and then clusters core objects based on natural neighbor structure. Finally, reliable negative samples are selected according to clustering result. With FCCCSR algorithm, we propose a new method named FCCCSR_Glu for glutarylation sites identification. In this study, multi-view features are extracted and fused to describe peptides, including amino acid composition, BLOSUM62, amino acid factors and composition of k-spaced amino acid pairs. Then, reliable negative samples selected by FCCCSR and positive samples are combined to establish models and XGBoost optimized by differential evolution algorithm is used as the classifier. On the independent testing dataset, FCCCSR_Glu achieves 85.18%, 98.36%, 94.31% and 0.8651 in sensitivity, specificity, accuracy and Matthew's Correlation Coefficient, respectively, which is superior to state-of-the-art methods in predicting glutarylation sites. Therefore, FCCCSR_Glu can be a useful tool for glutarylation sites prediction and FCCCSR algorithm can effectively select reliable negative samples from unlabeled samples. The data and code are available on https://github.com/xbbxhbc/FCCCSR_Glu.git.

An analytical study on the identification of N-linked glycosylation sites using machine learning model

N-linked is the most common type of glycosylation which plays a significant role in identifying various diseases such as type I diabetes and cancer and helps in drug development. Most of the proteins cannot perform their biological and psychological functionalities without undergoing such modification. Therefore, it is essential to identify such sites by computational techniques because of experimental limitations. This study aims to analyze and synthesize the progress to discover N-linked places using machine learning methods. It also explores the performance of currently available tools to predict such sites. Almost seventy research articles published in recognized journals of the N-linked glycosylation field have shortlisted after the rigorous filtering process. The findings of the studies have been reported based on multiple aspects: publication channel, feature set construction method, training algorithm, and performance evaluation. Moreover, a literature survey has developed a taxonomy of N-linked sequence identification. Our study focuses on the performance evaluation criteria, and the importance of N-linked glycosylation motivates us to discover resources that use computational methods instead of the experimental method due to its limitations.

Evaluation of deep learning techniques for identification of sarcoma-causing carcinogenic mutations

The abnormal growth of human healthy cells is called cancer. One of the major types of cancer is sarcoma, mostly found in human bones and soft tissue cells. It commonly occurs in children. According to a survey of the United States of America, there are more than 17,000 sarcoma patients registered each year which is 15% of all cancer cases. Recognition of cancer at its early stage saves many lives. The proposed study developed a framework for the early detection of human sarcoma cancer using deep learning Recurrent Neural Network (RNN) algorithms. The DNA of a human cell is made up of 25,000 to 30,000 genes. Each gene is represented by sequences of nucleotides. The nucleotides in a sequence of a driver gene can change which is termed as mutations. Some mutations can cause cancer. There are seven types of a gene whose mutation causes sarcoma cancer. The study uses the dataset which has been taken from more than 134 samples and includes 141 mutations in 8 driver genes. On these gene sequences RNN algorithms Long and Short-Term Memory (LSTM), Gated Recurrent Units and Bi-directional LSTM (Bi-LSTM) are used for training. Rigorous testing techniques such as Self-consistency testing, independent set testing, 10-fold cross-validation test are applied for the validation of results. These validation techniques yield several metrics such as Area Under the Curve (AUC), sensitivity, specificity, Mathew's correlation coefficient, loss, and accuracy. The proposed algorithm exhibits an accuracy of 99.6% with an AUC value of 1.00.

The applications of deep learning algorithms on in silico druggable proteins identification

•

We developed the first deep learning-based druggable protein classifier for fast and accurate identification of potential druggable proteins.

•

Experimental results on a standard dataset demonstrate that the prediction performance of deep learning model is comparable to those of existing methods.

•

We visualized the representations of druggable proteins learned by deep learning models, which helps us understand how they work.

•

Our analysis reconfirms that the attention mechanism is especially useful for explaining deep learning models.

Introduction

The top priority in drug development is to identify novel and effective drug targets. In vitro assays are frequently used for this purpose; however, traditional experimental approaches are insufficient for large-scale exploration of novel drug targets, as they are expensive, time-consuming and laborious. Therefore, computational methods have emerged in recent decades as an alternative to aid experimental drug discovery studies by developing sophisticated predictive models to estimate unknown drugs/compounds and their targets. The recent success of deep learning (DL) techniques in machine learning and artificial intelligence has further attracted a great deal of attention in the biomedicine field, including computational drug discovery.

Objectives

This study focuses on the practical applications of deep learning algorithms for predicting druggable proteins and proposes a powerful predictor for fast and accurate identification of potential drug targets.

Methods

Using a gold-standard dataset, we explored several typical protein features and different deep learning algorithms and evaluated their performance in a comprehensive way. We provide an overview of the entire experimental process, including protein features and descriptors, neural network architectures, libraries and toolkits for deep learning modelling, performance evaluation metrics, model interpretation and visualization.

Results

Experimental results show that the hybrid model (architecture: CNN-RNN (BiLSTM) + DNN; feature: dictionary encoding + DC_TC_CTD) performed better than the other models on the benchmark dataset. This hybrid model was able to achieve 90.0% accuracy and 0.800 MCC on the test dataset and 84.8% and 0.703 on a nonredundant independent test dataset, which is comparable to those of existing methods.

Conclusion

We developed the first deep learning-based classifier for fast and accurate identification of potential druggable proteins. We hope that this study will be helpful for future researchers who would like to use deep learning techniques to develop relevant predictive models.

A comprehensive tool for accurate identification of methyl-Glutamine sites

Methylation is a biochemical process involved in nearly all of the human body functions. Glutamine is considered an indispensable amino acid that is susceptible to methylation via post-translational modification (PTM). Modern research has proved that methylation plays a momentous role in the progression of most types of cancers. Therefore, there is a need for an effective method to predict glutamine sites vulnerable to methylation accurately and inexpensively. The motive of this study is the formulation of an accurate method that could predict such sites with high accuracy. Various computationally intelligent classifiers were employed for their formulation and evaluation. Rigorous validations prove that deep learning performs best as compared to other classifiers. The accuracy (ACC) and the area under the receiver operating curve (AUC) obtained by 10-fold cross-validation was 0.962 and 0.981, while with the jackknife testing, it was 0.968 and 0.980, respectively. From these results, it is concluded that the proposed methodology works sufficiently well for the prediction of methyl-glutamine sites. The webserver's code, developed for the prediction of methyl-glutamine sites, is freely available at https://github.com/s20181080001/WebServer.git. The code can easily be set up by any intermediate-level Python user.

iTAGPred: A Two-Level Prediction Model for Identification of Angiogenesis and Tumor Angiogenesis Biomarkers

A crucial biological process called angiogenesis plays a vital role in migration, growth, and wound healing of endothelial cells and other processes that are controlled by chemical signals. Angiogenesis is the process that controls the growth of blood vessels within tissues while angiogenesis proteins play a significant role in the proper working of this process. The balancing of these signals is necessary for the proper working of angiogenesis. Unbalancing of these signals increases blood vessel formation, which causes abnormal growth or several diseases including cancer. The proposed work focuses on developing a two-layered prediction model using different classifiers like random forest (RF), neural network, and support vector machine. The first level performs in silico identification of angiogenesis proteins based on the primary structure. In the case the protein is an angiogenesis protein, then the second level predicts whether the protein is linked with tumor angiogenesis or not. The performance of the model is evaluated through various validation techniques. The model was evaluated using k-fold cross-validation, independent, self-consistency, and jackknife testing. The overall accuracy using an RF classifier for angiogenesis at the first level was 97.8% and for tumor angiogenesis at the second level was 99.5%, ANN showed 94.1% accuracy for angiogenesis and 79.9% for tumor angiogenesis, and the accuracy of SVM for angiogenesis was 78.8% and for tumor angiogenesis was 65.19%.