A bioinformatics guide to Metabolomic Data analysis interpretation

#guide #metabolomics #data #interpretation
In this video, I have explained how we can interpret the results of metabolomics data and figures provided in research articles.
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[@elliealy4603]

Assalam anlaikum Dr. Assif! Please I just got my data from the company. Could you please guide me on how should i analyzed it, which data are more important? About the analysis should I just selected some figures from the data and talk about it. Here is how I received the data. 1) Data -neg_measurements -pos_measurements 2) Basic Analysis -Data Predeal -Sample Comparison -Multivariate Statistical Analysis -Metabolite Diff Analysis 3) Advanced Analysis -KEGG Annotation -KEGG Enrichment -METPA -Cluster -Metabolite Correlation -Metabolite Volcano -Compound Class -Ipath -Venn

[@asifmolbio]

Wslam company should already have analyzed is't it so? I think you jsut need to interpret

[@elliealy4603]

@@asifmolbio Thank you, God bless you

[@Hameedenv72]

Thank you for this informative video

[@asifmolbio]

Glad you like it

[@lifeislife715]

My (1) question 🙋🏻‍♂️ is if my organism doesn’t have KEGG pathway then what should I do in this case ? (2) question is company give you data 📊 figures etc already analyzed from metabo analyst ? Or you have to analyze in this website after getting your data from company in report form ? Kindly answer thx 🙏

[@asifmolbio]

Usually company give you already analyzed data including ready made figures

[@asifmolbio]

Then databases of model species are matched and searched

[@lifeislife715]

Thanks 🙏

[@tayyabsattarvlogs]

Informative video dr sb…❤

[@asifmolbio]

Glad you like it

[@Beautifullife7189]

Sir , Demo of metaboanalyst with one example

[@asifmolbio]

Sure, thanks for suggesting a potential topic.

[@namratakunwar9511]

For pathway analysis like picrust do we need to tell lab to do it separately or it comes under 16SrRNA sequencing?

[@asifmolbio]

Yes needs to

[@lifeislife715]

Nice 👍🏼

[@asifmolbio]

Thanks for the visit

[@sreeram6416]

sir could you help me with a small query. Actually from the ECLIP data I have found out which all circular rna are bound to my protein. Now I want to perform the pathway or network analysis of the circular rna and the rna binding protein complex, could you tell me just how to proceed

[@asifmolbio]

You can use SR Plot website

[@asifmolbio]

You can proceed with pathway or network analysis of the circular RNA (circRNA) and RNA-binding protein (RBP) complex: ### 1. **Prepare Your Data** Ensure you have the following data: - List of circRNAs bound to your protein. - Known or predicted interactions between your RBP and the circRNAs. - Functional annotations for the circRNAs (e.g., Gene Ontology terms, KEGG pathways). ### 2. **Identify Target Genes of circRNAs** circRNAs often function by interacting with miRNAs or directly with other RNAs/proteins. You can use databases and tools to predict or identify target genes: - **circBase**: For information on known circRNAs and their potential interactions. - **miRanda**, **TargetScan**, or **miRDB**: For predicting miRNA targets of circRNAs, if applicable. ### 3. **Functional Annotation and Pathway Enrichment Analysis** Use functional annotation tools to understand the biological roles of your circRNAs and their target genes: - **DAVID (Database for Annotation, Visualization, and Integrated Discovery)**: For functional annotation and pathway enrichment analysis. - **g:Profiler**: For functional profiling of gene lists with pathways and ontology terms. - **KEGG (Kyoto Encyclopedia of Genes and Genomes)**: For pathway analysis. - **Reactome**: For detailed pathway annotations. ### 4. **Network Analysis** Visualize and analyze the interactions between circRNAs, their target genes, and your RBP using network analysis tools: - **Cytoscape**: A powerful tool for visualizing complex networks and integrating various types of data. - **STRING**: Can be used within Cytoscape for protein-protein interaction networks. - **ClueGO**: A Cytoscape plugin for functional enrichment analysis and visualization of non-redundant biological terms. - **cytoHubba**: To identify hub genes and key nodes in your network. ### 5. **Building the Network** - **Import Data**: Load your circRNA, RBP, and target gene interaction data into Cytoscape. - **Create Network**: Construct the network by defining nodes (circRNAs, RBPs, and target genes) and edges (interactions between them). - **Annotate Nodes and Edges**: Use functional data to annotate the nodes and edges to add biological context. ### 6. **Analysis and Interpretation** - **Identify Key Players**: Use network centrality measures (e.g., degree, betweenness) to identify key circRNAs and proteins. - **Functional Modules**: Identify modules or clusters within the network that are enriched for specific functions or pathways. - **Visualization**: Create informative visualizations to present your findings. ### 7. **Validation and Further Experiments** Consider validating key interactions experimentally through techniques such as: - **qRT-PCR**: To verify the expression of circRNAs. - **RIP (RNA Immunoprecipitation)**: To confirm the interaction between your RBP and circRNAs. - **Luciferase Assays**: To validate miRNA interactions if applicable. By following these steps, you can perform a comprehensive pathway and network analysis of the circRNA and RBP complex, providing insights into their biological roles and interactions. If you need specific help with any step, let me know!

[@sreeram6416]

Bahut bahut dhanyavaad sir. Allah bless you sir.

[@Hameedenv72]

I have question regarding heat-map, it the value is less than 1 it will be down regulated and of positive one it will be up regulated? Thanks

[@asifmolbio]

Yes you said right

[@asifmolbio]

How to calculate fold change FC, log2FC, Pvalue, Padj, Up and down regulated genes kzbin.info/www/bejne/fnmWfp-iabxojac

[@asifmolbio]

Here you go 👉

[@Hameedenv72]

Thank you dr sb . Glad i found your video very informative and upto the marks

[@namratakunwar9511]

do we need to tell lab separately to do metabolomics analysis or check for metabolites also or does it all come under 16S rRNA sequencing or any other sequencing they used?

[@asifmolbio]

Need to tell separately

[@namratakunwar9511]

ok so if we ask them to do 16S rRNA sequencing only then what results do we get?Will we get the pathway analysis also or we need to tell them to do that also separately kindly reply🙏

[@Hameedenv72]

How i can view individual compound on metaboanalyst?

[@asifmolbio]

After you will do statistical analysis, it will generate a list of metabolites each is clickable and can view individual metabolites

[@Hameedenv72]

Thank you so much for reply, You mean in pls da the based on vip value the violon or box plot are showing ? But i saw in your presentation there was a bar plot,

[@asifmolbio]

@@Hameedenv72 yes based on VIP value

[@Hameedenv72]

Thank you dr,

[@asifmolbio]

@@Hameedenv72 welcome

[@ayazahmad1245]

Dear Dr Asif, Can I get your wechat id? I have some queries regarding pathway analysis. Thanks

[@asifmolbio]

asifalikalas

[@asifmolbio]

here is my we chat ID