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How can you use pathway analysis to identify key biological processes in bioengineering?

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Pathway analysis is a powerful tool to explore the complex interactions and functions of genes, proteins, metabolites, and other molecules in bioengineering. By using pathway analysis, you can identify the key biological processes that are involved in your bioengineering project, such as designing synthetic circuits, engineering biomaterials, or optimizing bioreactors. In this article, you will learn how to use pathway analysis to enhance your bioengineering skills and outcomes.

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Michel Popielarz

snr Business Development

1 What is pathway analysis?

Pathway analysis is a method to study the biological pathways that are relevant to a specific condition, phenotype, or experiment. A pathway is a set of molecules that interact with each other to perform a certain function, such as signal transduction, metabolism, or gene regulation. Pathway analysis can help you to discover the molecular mechanisms, regulatory networks, and functional modules that underlie your bioengineering problem. You can use pathway analysis to compare different conditions, such as normal and diseased states, or different treatments, such as drugs and stimuli.

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Michel Popielarz

snr Business Development
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analysis of the different pathways corresponds to identifying phenotypic differences between 2 states. healthy / sick, or treated / untreated, for example. The analysis is generally complex and can be costly, as the more parameters are measured, the greater the chance of finding the relevant ones, but the more complex it is to control the quality of the results, their analysis and interpretation.

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Siva Kumar Panguluri

Associate Professor, Department of Pharmaceutical Sciences, University of South Florida, Tampa, FL
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By developing cellular pathways from your data (genes or molecular). Then looking at the commonly regulated molecule or gene in most of the cellular pathways or networks you developed from your data. Validating it's expression using other techniques.

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Jo?o Oliveira

Engenheiro Biomédico | Engenheiro Clínico | Gest?o de Tecnologias em Saúde | Engenheiro de Seguran?a do Trabalho
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Penso que a análise de caminhos é uma abordagem poderosa para investigar as intera??es moleculares em sistemas biológicos. Acredito que ao identificar e analisar as vias específicas envolvidas em uma condi??o ou fenótipo, é possível compreender melhor os mecanismos subjacentes e potenciais alvos terapêuticos. Por exemplo, a análise de vias pode revelar diferen?as significativas entre o estado normal e patológico, fornecendo insights valiosos para o desenvolvimento de novas estratégias de tratamento em bioengenharia.

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2 How to perform pathway analysis?

To perform pathway analysis, you need a list of molecules of interest such as genes or proteins, and a database of pathways such as KEGG, Reactome, or BioCyc. Your list of molecules can be derived from various sources including gene expression, proteomics, metabolomics, or genome editing data. The database of pathways contains information about the structure, function, and annotation of the pathways. Different software tools such as Cytoscape, PathVisio, or GSEA can be used to perform pathway analysis. The basic steps include uploading your list of molecules and selecting the database of pathways to identify enriched or activated pathways using statistical methods like Fisher's exact test, hypergeometric test, or gene set enrichment analysis. Graphical methods like network diagrams, heatmaps, or bar charts can then be used to visualize and explore the pathways and their interactions. Finally, you can interpret and validate the results using biological knowledge, literature, or experiments.

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Michel Popielarz

snr Business Development
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Bear in mind is that the genome (DNA) is generally stable (genomics), RNAs are generally unstable (transcriptomics), proteins are the really operational elements (proteomics). they act and they build. The result of all this, however, is the set of small molecules needed to synthesize the genome, RNA and proteins, and the result of their degradation. The science of all these small molecules is metabolomics. It is by far the most complex, but also the most informative. Last but not least, there are all the molecules that come from what we breathe, eat, drink, touch (cosmetics) and also from our microbiota. They have a huge influence on our self. Ideally, all these factors should be measured and analyzed, but this comes at a cost.

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3 Why is pathway analysis useful for bioengineering?

Pathway analysis can be used to achieve various goals in bioengineering, such as designing synthetic circuits, engineering biomaterials, and optimizing bioreactors. For example, you can use pathway analysis to identify the optimal components and connections for a synthetic circuit based on its desired function or to understand how a biomaterial interacts with its biological environment. Additionally, pathway analysis can be used to evaluate the performance and robustness of a synthetic circuit by comparing it with natural pathways, optimize the properties and functions of a biomaterial by modifying its molecular composition or structure, monitor and control the metabolic and physiological state of a bioreactor, and improve the efficiency and stability of a bioreactor by adjusting culture conditions or engineering microorganisms.

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Michel Popielarz

snr Business Development
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It is not useful, it is essential. The problem is that it is expensive, and to get relevant results you have to do things right. I have personally seen famous scientists spend fortunes on samples of zero quality (without mastering their collection, storage, age, etc.). You have to work with the right lab. You have to validate your methods. You have to trust your employees.

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4 What are the challenges and limitations of pathway analysis?

Pathway analysis is not a perfect method and has some challenges and limitations that you need to be aware of. Data quality and quantity are important for accurate and reliable results, as is considering the complexity and diversity of pathways. Additionally, pathway databases may not be complete or comprehensive, so you should check the annotation and update accordingly. To ensure success in your bioengineering problem, you should cross-validate results across multiple databases and methods, as well as supplement with other sources.

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5 How to learn more about pathway analysis?

Pathway analysis is a rapidly evolving and expanding field, and there are many resources and opportunities to learn more about it. You can find online courses and tutorials, such as Coursera or edX, or software tools and databases, such as Cytoscape or PathVisio, that provide their own tutorials and manuals. Additionally, you can read books and journals that cover the theory and practice of pathway analysis, such as Pathway Analysis for Drug Discovery or Computational Methods in Systems Biology. To stay up-to-date with the latest research and developments in pathway analysis, you can browse journals like BMC Systems Biology or PLOS Computational Biology. Furthermore, you can attend workshops and conferences that offer hands-on training and networking opportunities in pathway analysis, such as ISMB or ECCB. Finally, you can participate in challenges and competitions that test your skills in pathway analysis, like DREAM or CASP.

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6 Here’s what else to consider

This is a space to share examples, stories, or insights that don’t fit into any of the previous sections. What else would you like to add?

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How can you use pathway analysis to identify key biological processes in bioengineering?

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1 What is pathway analysis?

2 How to perform pathway analysis?

3 Why is pathway analysis useful for bioengineering?

4 What are the challenges and limitations of pathway analysis?

5 How to learn more about pathway analysis?

6 Here’s what else to consider

Bioengineering

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