Reactome Pathway Analysis Demo-Fall2020

[@mohamadhasanansarizadeh7420]

signal transduction and gene expression alway light up, so don't pay anetion to those that much. So, which one do we care? the ones which are more light up

[@biologybasics]

Yes, you need to pay attention to the ones that light up related to specific networks of interest. This video was done to introduce the software to undergraduate students. If you are interested in learning this software for research purpose I can make a more detailed and in-depth video to show it's capabilities.

[@poojasingh-zf8rz]

I have differential whole proteome data of an insect of lepidopteran class. now I would like to know the interaction between downregulated , upregulated , unaffected proteins, if any. Can you please tell is this possible to use this browser for abovesaid purpose and how??

[@biologybasics]

sure, will try to do one in the next couple of days with some example data set.

[@biologybasics]

I apologize for the delay in getting that video ready. I have been sick. If you have differential data, you can definitely use it to do the above said analysis using reactome. You can also simplify it further by first semi-analyzing it excel. For that purpose, you would convert the data to fold change compared to control for your experimental samples. Then, I would make a short list for reactome that shows just the proteins that were at least 2 fold up or down regulated as input. That would make it more manageable. However, you can use the entire set as is as well as long as it is in the right format as a text file.

[@biologybasics]

while reactome may not have your actual insect/ class information, it will still give you insight into the pathways and networks affected in your specific system.

[@adekunleajiboye1244]

Hi. My study focuses on inflammation but I am not seeing any pathways in my gene ontology result that relate to inflammation. Please what should I do?

[@MamaMimiNMe]

Have you input the gene ontology results in reactome to see what comes up? Sometimes individual genes may not be directly related to a process but a combination of them together can indeed affect the pathway of interest indirectly.

[@adekunleajiboye1244]

@@MamaMimiNMe Thanks. How do you mean?

[@poojasingh-zf8rz]

btw it was an Informative video.

[@nahuelcesattilaluce1257]

I found the video very useful actually. The only one thing that I have to suggest is, please, minimize the participant's windows...there is not sense to have a little window of every person in the class, and its annoying because it obtaculize constantly what teacher is showing.

[@MamaMimiNMe]

Thank you for your suggestion. I will definitely keep that in mind in future class recordings. I am glad you found the information useful.