Oncol. Quercetin hinders microglial activation to alleviate neurotoxicity via the interplay between NLRP3 inflammasome and mitophagy. J. Stat. The PD dataset was obtained from the public repository NCBI GEO (http://www.ncbi.nlm.nih.gov/geo) (Barrett et al., 2013) using Parkinsons disease or Parkinson as keywords for the search. A role for 12-lipoxygenase in nerve cell death caused by glutathione depletion. A study has shown that E2 can activate autophagy by regulating the expression of UKL1, thereby preventing the -abnormal accumulation of synuclein and exerting a neuronal protective effect (Varmazyar et al., 2019). 6, 49. doi:10.1038/s41392-020-00428-9, Ye, M., Luo, G., Ye, D., She, M., Sun, N., Lu, Y. J., et al. PTGS2 (COX2), a neuroinflammatory marker (NMS), plays a role in the occurrence of neurodegenerative diseases (Hoozemans et al., 2008). The peroxisome is an important organelle in this signaling pathway, and its biogenesis starts from the early peroxidase pex3, which can participate in key processes such as free radical detoxification (Wanders and Waterham, 2006). Inhibition of neuronal ferroptosis protects hemorrhagic brain. Tcmsp: A database of systems pharmacology for drug discovery from herbal medicines. (2016). The HERB (http://herb.ac.cn/) (Fang et al., 2021) database is a natural medicine database platform that integrates high-throughput experimental data and reference mining data. Bioinformatics 31, 29122914. Regulated necrosis: Disease relevance and therapeutic opportunities. (A) lasso regression analysis; (B) number of features predicted by SVM-RFE; (C) Venn diagram of LASSO and SVM-RFE; (D) ROC evaluation of intersecting genes. Manuscript review and editing were performed by ML, SL, and MY. (2023). Curr. Objective: Ferroptosis, a novel form of cell death, is closely associated with excessive iron accumulated within the substantia nigra in Parkinsons disease (PD). Read papers from the ISCB Find out more Computational biology and bioinformatics is an interdisciplinary field that develops and applies computational methods to analyse large collections of biological data, such as genetic sequences, cell populations or protein samples, to make new predictions or discover new biology. Ferroptosis is considered a novel form of regulated cell death resulting from severe lipid peroxidation and depends on reactive oxygen species (ROS) production and iron overload (Dixon et al., 2012; Do Van et al., 2016).
Uncovering ferroptosis in Parkinson's disease via bioinformatics and biology problems: sequence analysis, structure or function prediction, data mining, etc. (2023). After analysis of internode relationships in the string network diagram using Perl imported into Cytoscape v3.7.1, the intersecting genes were calculated with the built-in cytoHubba plugin. Int. Thank you for visiting nature.com. Subsequently, to further predict the ferroptosis feature genes for PD, we predicted and classified 109 ferroptosis differential genes using two machine learning models, Lasso regression and SVM-RFE. Red circles represent overlapping genes between LASSO and SVM-RFE; orange diamond represents active ingredient. Eur. Psychiatry 79, 368376. Signal Transduct. Identification and analysis of key genes in osteosarcoma using bioinformatics. . Here, we employed a bioinformatics and machine learning approach to predict the genes associated with ferroptosis in PD and investigate the interactions between natural products and their active ingredients with these genes. Transl. This study is the first to integrate bioinformatics analysis methods, machine learning model prediction classification, and data mining-based inverse derivation of active ingredients, screen core compounds of feature gene action derived from machine learning predictions, and validate using molecular docking. OMICS 16, 284287. Cellular response to oxidative stress refers to any process that changes cell state or activity due to oxidative stress, usually caused by exposure to high levels of reactive oxygen species, such as superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. Nutr. Despite extensive research, the underlying molecular mechanisms driving ferroptosis in PD remain elusive. Heres how to avoid their pitfalls. Cyclooxygenase-1 and -2 in the different stages of Alzheimer's disease pathology. Eur.
Ten quick tips for avoiding pitfalls in multi-omics data integration Furthermore, we aim to identify natural products that can potentially treat PD. doi:10.1371/journal.pgen.0030098, Li, Q., Han, X., Lan, X., Gao, Y., Wan, J., Durham, F., et al. Detailed docking information was visualized using igplot + v.2.1 (Ye et al., 2021). The DEGs were visualized by volcano plots and heatmaps (Figures 3AF).
Modelling capture efficiency of single-cell RNA-sequencing data doi:10.1089/omi.2011.0118, Zecca, L., Gallorini, M., Schunemann, V., Trautwein, A. X., Gerlach, M., Riederer, P., et al. PDFerDEGs logFC functional enrichment. Figures 9FJ shows the amino acid residue information versus hydrogen bonding distance for the docking of each compound to proteins. Biomed. (2009). Sci. 13, 1117987. doi:10.3389/fcimb.2023.1117987, Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., et al.
Bioinformatics Methods | From Omics to Next Generation Sequencing | Sh FIGURE 3. J. Pharmacol. TLR4 is one of the key targets of inflammasomes triggered by the Toll-like receptor signaling pathway in the KEGG pathway, which not only participates in neuroinflammation but also induces necroptosis (Netea et al., 2009). We present an algorithm, SComatic, that can be used to directly detect somatic mutations in single-cell data sets without using a reference sample. Methods: We comprehensively analyzed differentially expressed genes (DEGs) for ferroptosis associated with PD (PDFerDEGs) by pairing 3 datasets (GSE7621, GSE20146, and GSE202665) from the NCBI GEO database and the FerrDb V2 database.
Next-generation microbiology: from comparative genomics to gene Sequence analysis This study aimed to identify the crosstalk genes between SLE and VTE and explored their clinical value and molecular mechanism initially.MethodsWe downloaded microarray datasets of SLE and VTE from the Gene Expression Omnibus (GEO) dataset. (2011). Copyright 2023 Wang, Chen, Tang, Wang, Gong, Li, Li and Yang.
Identification and comprehensive analysis of ferroptosis - PubMed doi:10.1182/blood-2003-03-0672, Gustavsson, E. K., Zhang, D., Reynolds, R. H., Garcia-Ruiz, S., and Ryten, M. (2022). E2 has protective effects against many neurodegenerative diseases and mediates its effects through dopamine receptors (Brann et al., 2007; Varmazyar et al., 2019). These findings demonstrate that 109 DEGs can be involved in ferroptosis-related processes, demonstrating the potential of these target genes as research targets. 34, 532549.
Nanopore sequencing technology, bioinformatics and applications (2007). (2001). Neurodegener. Neuron 19, 453463. The machine learning model prediction was used to identify the feature genes, which were then combined with natural products of traditional Chinese medicine to explore potential therapeutic agents. Epidemiological studies reveal that young-onset PD (onset age <40years) is on the rise in China and Europe, posing a serious threat to human health (Jankovic, 2008). (2011). As a result (Table 5), the top five ingredients could all interact with the six hub genes. Microarray data for each GEO dataset can be obtained using R package GEOquery. Ferroptosis is a novel form of iron-dependent and reactive oxygen species (ROS)-dependent cell death, which is distinct from apoptosis, necrosis, and autophagy.
Introduction to bioinformatics - PubMed After the computational results were exported, the R package UpSetR (Conway et al., 2017) was used to score hub genes and finally obtain the core intersection genes. AutoDock Vina 1.2.0: New docking methods, expanded force field, and Python bindings. The pathological mechanism of PD is multifactorial, involving the death of dopaminergic neurons resulting from complex interactions between abnormal -synuclein aggregation, mitochondrial and lysosomal dysfunction, and neuroinflammation (Bloem et al., 2021; Wang et al., 2022). JCI Insight 2, e90777. doi:10.2174/138161208784480171, Iranpour, N., Zandifar, A., Farokhnia, M., Goguol, A., Yekehtaz, H., Khodaie-Ardakani, M. R., et al.
Neuroimaging feature extraction using a neural network classifier for Med. The datasets presented in this study can be found in online repositories. However, an imbalance in iron homeostasis, such that free iron exerts toxic effects, catalyzes the Fenton reaction and produces damaging reactive free radicals, causing oxidative stress and, ultimately, dopaminergic neurons (Ganz, 2003). Hum. Figure 9I shows that trans resveratrol formed 1 hydrogen bond with Tyr373 and Gln374 in PTGS2. 3) Defining docking parameters: We imported the protein receptors and small molecule receptors separately into AutoDock Vina to determine the scope of molecular docking. (2017). Curr. The result of eliminating batch effects.
Explainable AI for Bioinformatics: Methods, Tools, and Applications Finally, we mapped a network combined with ingredients and signature genes, then carried out molecular docking validation of core ingredients and targets to uncover potential therapeutic targets and ingredients for PD. Nat. general definition: computational techniques for solving biological problems data problems: representation (graphics), storage and retrieval (databases), analysis (statistics, artificial intelligence, optimization, etc.) Demographic-prediction algorithms have various challenges, following best practices can minimize the harms. After eliminating batch effects across datasets, the three datasets were merged to obtain a total of 55 PD samples and 49 normal control samples (Table 1). This dataset analyzed the brain substantia nigra tissue of 9 normal samples and 16 PD samples after death. Neurobiol. Sci. (2015). For instance, several mutations in ferroptosis genes are associated with PD, including the key regulator of ferroptosis DJ-1, autosomal recessive PD gene PARK7 and PLA2G6 (Cao et al., 2020). Differential gene expression analysis to identify DEGs can be performed with R package limma (Ritchie et al., 2015).
Using Dali for Protein Structure Comparison | SpringerLink Tocopherol had the smallest binding energy to ADIPOQ but could not exhibit its hydrogen bond, so we selected the docking results of PTGS2 for visualization. 14, 14191427. Cell Death Discov. Mol. Differential requirement for the activation of the inflammasome for processing and release of IL-1beta in monocytes and macrophages. 3, e98. 17 beta estradio has the smallest binding energy to Atg7. High-throughput can help us better understand the complexity and diversity of biological systems, gives us a clearer understanding of gene expression profiles in living organisms. Biochim. Proc. Analytical validation and implementation of a pan cancer next-generation sequencing panel, CANSeq(TM)Kids for molecular profiling of childhood malignancies. Bioinformatics 38, 38443846. 139 (Suppl. In the present study, we analyzed 3 integrated transcriptome datasets and found 109 DEGs related to ferroptosis in PD, and the related pathways were identified by GO and KEGG analyses. Deep learning is used to accelerate the inference of genetic clusters, allowing the analysis of hundreds of thousands of human genomic datasets in a computationally efficient way. Chem. Finally, you will learn how to apply popular bioinformatics software tools to reconstruct an evolutionary tree of ebolaviruses and identify the source of the recent Ebola epidemic that . Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous progress in the understanding of cellular mechanisms, disease progression, and the relationship between genotype and phenotype.
The past three decades have witnessed an explosion of what is now referred to as high-dimensional `omics' data. To perform GO and KEGG enrichment analysis of the intersection genes, we utilized version 3.18.1 of the R package clusterProfiler (Yu et al., 2012), with a p-value threshold of less than 0.05. Shandong University of Traditional Chinese Medicine, China, The First Affiliated Hospital of Kunming Medical University, China, China Academy of Chinese Medical Sciences, China. Subsequently, we used the R package sva to remove batch effects, resulting in 49 control samples and 55 PD samples. Am. After this step, we exported the docking result file in Vina Config format. TRAM couples endocytosis of Toll-like receptor 4 to the induction of interferon-. Omics 19, 218228. These findings might pave the way for future research in this area. A., and Bush, A. I. Sepsis-induced adipokine change with regard to insulin resistance. Bioinformatics methods are also used to assign functions to uncharacterized genes which can be targeted as a candidate in vaccine design and can be a better approach toward the inclusion of women that are pregnant into vaccine trials and programs. Metal ion transporters are involved in maintaining the required levels of various metal ions in the cell (Bowers and Srai, 2018). Besides, the top five core ingredients were obtained according to calculation result. According to the network, top 5 core active ingredients (quercetin, 17-beta-estradiol, glycerin, trans-resveratrol, and tocopherol) were molecularly docked to hub genes to reveal their potential role in the treatment of ferroptosis in PD. Recent research has demonstrated that natural products have potential anti-Parkinsons disease (PD) effects, attributable to their antioxidant and anti-inflammatory properties, as well as their ability to inhibit iron accumulation and maintain proteasome degradation and mitochondrial homeostasis (Solayman et al., 2017; Zhang et al., 2017). Human cyclooxygenase-2 cDNA. 1), 179197. Hub genes of the Overlapping Gene PPI network. Figure 9H shows that glycerin formed 2 hydrogen bonds with Gln241, Gly235 and Arg333 in PTGS2. Proliferative DR (PDR) is the aggressive stage of DR with angiogenesis as a pathological hallmark, which is the main cause of blindness. Steroids 72, 381405. Trans resveratrol has the smallest binding energy to PTGS2. An innovative journal that provides a forum for new discoveries in bioinformatics. Article CAS Google . Validation and application of new NGS-based HLA genotyping to clinical diagnostic practice. In this edition, four new chapters are included and two chapters are updated. Iron ions, as one of the metals whose homeostasis is essential for the physiological function of the brain, perturbed homeostasis, may be responsible for causing specific local cell death. Figure 9F shows that quercetin formed 1 hydrogen bond with Asn124, Pro77 and Thr390, and 2 hydrogen bonds with Leu185 in FADS2. doi:10.1111/jpc.14292, Healy, S., McMahon, J., Owens, P., and FitzGerald, U. PDFerDEGs logFC enrichment analysis. (2023). doi:10.1039/d2mo00267a, Yu, G., Wang, L. G., Han, Y., and He, Q. Y. doi:10.1093/nar/28.1.235, Bersuker, K., Hendricks, J. M., Li, Z., Magtanong, L., Ford, B., Tang, P. H., et al. Structural Bioinformatics Protocol Using Dali for Protein Structure Comparison Liisa Holm Protocol First Online: 01 February 2020 4217 Accesses 256 Citations 14 Altmetric Part of the Methods in Molecular Biology book series (MIMB,volume 2112) Abstract The datasets used in this study. Regularization paths for generalized linear models via coordinate descent. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide (2000). Med. A., et al. Detecting somatic mutations in single-cell data sets, Machine learning speeds up genetic structure analysis, Human-caused wolf mortality persists for years after discontinuation of hunting, Aluminum surface defect detection method based on a lightweight YOLOv4 network, Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics, Leveraging spatial transcriptomics data to recover cell locations in single-cell RNA-seq with CeLEry, A comparison of different machine-learning techniques for the selection of a panel of metabolites allowing early detection of brain tumors, Transformer-based hand gesture recognition from instantaneous to fused neural decomposition of high-density EMG signals, Computer algorithms infer gender, race and ethnicity. Struct. Investigation of this coding gene in PD has not been reported, which deserves our attention.
What is bioinformatics? A proposed definition and overview of - PubMed Des. Notably, we performed data mining based on reverse derivation for natural products related to the 29 feature genes and clarified the top 5 core active ingredients according to the Overlapping Genes-Ingredients network, followed by molecular docking for validation, suggesting that quercetin, 17-beta-estradiol, glycerin, trans-resveratrol, and tocopherol might serve as potential therapeutic agents against the ferroptosis process of PD. (2019). 14, 1067457. doi:10.3389/fgene.2023.1067457, Sertbas, M., and Ulgen, K. O. doi:10.1093/bioinformatics/btx364, Dachert, J., Ehrenfeld, V., Habermann, K., Dolgikh, N., and Fulda, S. (2020). doi:10.1016/s0140-6736(21)00218-x, Boots, A. W., Haenen, G. R., and Bast, A. Acta 1771, 10311045. J. Med. (2020). Nucleic Acids Res. doi:10.1016/j.steroids.2007.02.003, Burguillos, M. A., Deierborg, T., Kavanagh, E., Persson, A., Hajji, N., Garcia-Quintanilla, A., et al. We ranked them according to MCC, DMNC, MNC, Degree, BottleNeck, EcCentricity, Closeness, Radiality, Betweenness and Stress scoring (Table 3). The lack of in vivo and in vitro experiments to validate the regulatory relationship between the feature genes derived from the screen and natural products against ferroptosis in PD is a noteworthy limitation. Molecular docking binding energy. In particular, we will use methods from computational proteomics to ask how we could assess whether this result is valid or due to some form of contamination. Patterns and costs of health-care utilisation in Australian children: The first 5 years. Neurotrophic and neuroprotective actions of estrogen: Basic mechanisms and clinical implications.
Bioinformatic Methods I | Coursera 106, 1559S1566S. (AC) functional enrichment of GO; (D) result of KEGG; (E) Sankey diagram combined with GO and KEGG; (F) overall result of GO related to ferroptosis. also called computational biology HLA 101, 496506. Acad. Iron, neuromelanin and ferritin content in the substantia nigra of normal subjects at different ages: Consequences for iron storage and neurodegenerative processes. FIGURE 9. Biochim. 14:1231707. doi: 10.3389/fgene.2023.1231707. 15, 27892794. Data collection and analyzation were performed by PW, QC, BG, LW, and ZT.
Computational biology and bioinformatics - Nature This package is characterized by fitting a range of different values to each previous fit, resulting in significant improvements in operational efficiency.
"Bioinformatics: Introduction and Methods," a Bilingual Massive Open 15, 59. doi:10.1186/s13024-020-00408-1, Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., et al. Ferroptosis, a newly characterized form of cell death in Parkinson's disease that is regulated by PKC. Nucleic Acids Res. doi:10.1093/nar/gkv007, Robin, X., Turck, N., Hainard, A., Tiberti, N., Lisacek, F., Sanchez, J. C., et al. Z., Xu, S., Li, H., Belaidi, A. (2016). The manuscript was drafted by PW, QC, LW, and BG. Atg7 deficiency in microglia drives an altered transcriptomic profile associated with an impaired neuroinflammatory response. doi:10.2174/1389200217666160709204826, Sterling, J. K., Kam, T. I., Guttha, S., Park, H., Baumann, B., Mehrabani-Tabari, A. A review of genome-wide transcriptomics studies in Parkinson's disease. doi:10.1093/bioinformatics/btv300, Wan, Z., Mah, D., Simtchouk, S., Klegeris, A., and Little, J. P. (2014). Here, the authors propose GlycanFinder, a database search and de novo sequencing tool for the analysis of intact glycopeptides. Currently, although there are individual bioinformatics reports and studies on ferroptosis in PD, the development of compound prediction based on machine learning has not been reported (Moni et al., 2019; Falchetti et al., 2020; Jian et al., 2022). Blood 102, 783788. After identification, 24 genes had corresponding ingredients (Supplementary Table S6). 9, 361368. Although PTGS2 also had related ingredients, the number was more than three thousand, and we thought that too many ingredients were not beneficial to this study, so we did not include the ingredients related to this gene. TABLE 5. Overlapping Genes-Ingredients network.
Bioinformatic Methods II | Coursera Immunol. Multidisciplinary methods through coalition of biological data with statistics are essential for this. To investigate the potential link between ferroptosis and PD, we initially retrieved iron-related genes from the ferrdb V2 (http://www.zhounan.org/ferrdb/current/) database, which compiles drivers, suppressors, and markers associated with ferroptosis, resulting in a total of 728 ferroptosis-related genes.
Genomic analysis - Latest research and news | Nature Here, the authors develop CeLEry, a machine learning method that aims to recover cell locations for single-cell RNA-seq data by leveraging information learned from spatial transcriptomics. Atom RSS Feed Computational biology and bioinformatics is an interdisciplinary field that develops and applies computational methods to analyse large collections of biological data, such as. nonparametric methods, including bootstrap and permutation tests; correlation, regression, ANOVA, and generalized linear models; preprocessing . Protein structure prediction by using bioinformatics can involve sequence similarity searches, multiple sequence alignments, identification and characterization of domains, secondary structure prediction, solvent accessibility prediction, automatic protein fold recognition, constructing three-dimensional models to atomic detail, and . Sci. While a variety of small molecules and natural products with anti-PD activity have been identified, including flavonoid and polyphenol compounds, phenylpropanoid (coumarin) compounds, quinone compounds, saponin compounds, alkaloid compounds, and terpenoid compounds, none of them are capable of completely curing PD (Solayman et al., 2017). They were quercetin (Ingredient ID:HBIN041721), 17-beta-estradiol (Ingredient ID:HBIN001991), glycerin (Ingredient ID:HBIN028102), trans-resveratrol (Ingredient ID:HBIN046831) and tocopherol (Ingredient ID:HBIN046506) (Table 4). (2016). Test and evaluate a computational algorithm.
Prediction of hub genes and key pathways associated with the - Nature Glycerin has the smallest binding energy to PTGS2. Cell Proteomics 13, 397406. Lett. 446, 3742. Iron neurochemistry in alzheimer's disease and Parkinson's disease: Targets for therapeutics. U. S. A. Furthermore, we calculated the Z-score for each item using the R package Goplot (Walter et al., 2015). Internet Explorer). The above three biological processes suggested that the enriched genes were associated with the imbalance of intracellular iron homeostasis in dopaminergic neurons and caused oxidative stress, which ultimately led to neuronal cell damage. Pharmacological basis and new insights of quercetin action in respect to its anti-cancer effects. We also downloaded the string database (https://string-db.org/), which was used to filter protein-protein interactions (PPIs) between the intersection genes of the machine learning model, with the minimum required interaction score set to 0.4 and hidden connected nodes in the network. We further propose a multivariate regression with priors specified in the Bayesian framework that allows for group sparsity at multiple levels including SNPs and genes. (2021).
An overview of bioinformatics methods for modeling biological pathways ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2. Nature 575, 688692.
Yellowstone Family Names,
Asu Theater Productions,
New Orleans Tv Reporters,
Used Kymco 50cc Scooter For Sale,
Cute Ways To Say I Want To See You,
Articles B