Volcano plots explained | How to interpret a volcano plot for DGE

In this video I will explain what is a volcano plot and how to interpret it when representing gene expression data.
Learn what is a volcano plot, how to quickly identify significant genes, and genes that are upregulated and downregulated.
Hope you like it!
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Watched it already?
If you liked this video or found it useful, please let me know! Your comments and feedback are very much appreciated😊
If you have questions, don't hesitate to leave me a comment down below, I will answer as soon as I can:)
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More volcano plots resources:
In this video, I explain how to create your own volcano plot in R:
• Volcano plots with ggp...
This is also a really cool tool made with RShiny which allows you to customise your own volcano plot online:
huygens.science.uva.nl/VolcaN...
And here is a nice, short explanation on how to interpret volcano plots:
www.htgmolecular.com/blog/202...

[@nathanieldanielrabo2423]

Exceptional. Thanks 🎉

[@mohamedirfan5480]

Keep making videos ma'am. This is the future of biotechnology. You are a saviour. God bless this channel!!

[@odothomas1851]

Amazing. Thank you

[@janahanke5420]

this video saved me... my assignment would have been a fail otherwise, thank you so much!!

[@sanariaaljaf9619]

This was such an informative video! Helped explain so much for me as I have never been exposed to Volcano plots before. Will definitely be tuning in more for more videos! Thank you.

[@asmaal-yousofi3165]

Very useful thanks

[@AzminaAlisa]

Easy and simple to understand! Thank you so much for your comprehensive guidance!

[@spalding5198]

You don’t know just how happy you’ve made me!
Thanks immensely for what you do!!!

[@AbhishekVerma-xw3lz]

3:16 The value of gene expression in B should be 6 instead of 9. On a side note, the video provides good explanation.

[@biorainbows4313]

What a great explanation! Thank you so very much :)

[@AyrodsGamgam]

every now and then you find a really nice video that explains something you have a struggle with because the idyot prof in class don't know how to explain it, and so this video is a gem and in a couple minutes does the unthinkable. Thank you Madam.

[@trixstandflipped]

Fantastic video explained in simple yet very applicable terms. Thank you!

[@manjinderkaur-hf5pb]

Very useful

[@raha1603]

As usual, it is very clearly explained and yet very informative, thanks.

[@vinton1881]

Clear explanation! Thank you

[@alejandrotorres8586]

Excellent explanation. Greetings from Mexico

[@martagarcia1946]

Amazing explanation! Thank you very much! Love all your videos, I can understand everything! :)

[@matheusalmeida773]

Fantastic explanation! Thank you very much!

[@lamaismaiel9870]

It is very nice and well-explained, thanks!

[@rayees.ahamed]

Well explained. Thank you.

[@MrAseem777]

Precise and clear..great effort.. waiting for such useful videos

[@nami17]

This was really helpful! Thank you :)

[@kiplimosimon1429]

I enjoyed the explanation. it is very clear. Thanks so much

[@zahraaalawadly8583]

The video is really so useful. Thank you!

[@muttugoudr2346]

thank you!

[@DarkBumbelsztein]

this video was so clear and so nice!!! thanks so much. PCA plots next, please!! a super lost Metabolomics student here

[@biostatsquid]

Hi Julia thank you very much, this means a lot! PCA plots definitely on the list;)

[@nehapimpalwar7339]

VERY INFORMATIVE VIDEO, THANKS A LOT IT MADE MY LIFR EASIER

[@MHiol1]

Thank you.

[@kibuasmr4423]

Awesome vid, thanks !

[@nasserbenomar]

thank you so much

[@ruthgyereh1052]

More than useful. You’re a star

[@maheshrani6609]

well explained....simple but very effective.

[@user-so6qc3gd5o]

That was incredible thank you :)

[@mobeenshaik9164]

keep on doing this beautiful work

[@JorgeCastillo-ko3im]

Very well explained. Easy to understand. Thank you.

[@biostatsquid]

Thank you! I'm glad it was useful:)

[@partha_plethorapedia]

very nice explanation...thank you.

[@koustavroy350]

Very clear presentation

[@lucianosouza6766]

it is a well done video. Thank you so much ;)

[@parsaarabshahi6600]

very useful
thank you!

[@biostatsquid]

Glad it was helpful!

[@user-if2di8gh1o]

amazing. thank u biostats squid

[@sanjaisrao484]

exellent thanks

[@debojittalukdar5196]

Extremely Good and helpful video....I need more videos on MA plot, PCA plot, Kegg ,Bubble plot and Heat Map Analysis..Please .

[@MsFireroll]

Very great ! But 9/3=2 ????

[@domi1096]

I was wondering the same...

[@AyrodsGamgam]

just a typo, she meant 6/2

[@gopalkalwan7465]

6/2 should be there because the purpose was to get 2 fold

[@shabihaheea39]

Very helpful

[@nidhisingh7066]

you explained this in a very nice way!!

[@biostatsquid]

Thank you Nidhi! Glad it helped:)

[@dr.tranngocthien]

thank you

[@anujvermabiotech]

Thanks

[@rabeeakhan563]

please make videos using multiple bioinformatics tools to interpret RNA seq data.

[@biostatsquid]

Thanks for your suggestion! Will definitely do:)

[@Claireshoon]

That's really clear and thank you: please next OPLS-DA

[@biostatsquid]

Glad you found it useful Shoon! And thanks for your suggestion, I will definitely add it to the list:)

[@folenspill]

Thank you for a very nice video. I have trouble understanding the fold change for gene 1 in the table example. Wouldn't the fold change (FC) be 3 (9 divided by 3) and log2(FC) 1.585?

[@biostatsquid]

Yes, apologies, that was a typo! You are correct:)

[@daniiujes9577]

What a video

[@user-io6wu9px2n]

the first example of gene 1 shows the value for A=3 and B=9 so the FC should be 3 of 2 ?????????? Im not sure but plz respond, i want to have a better understanding of the topic

[@biostatsquid]

Hi, thanks for your comment and sorry for the confusion, it's just a typo! What I meant to have there is expression in A = 3, expression in B = 6 (so twice the expression) -> 6/3 = 2 -> log2(2) = 1. Hope this makes sense now.

[@user-io6wu9px2n]

thank u @@biostatsquid

[@PerlaAlejandra009]

Always the side right is where are upregulating genes and the downregulated genes are in left side?

[@biostatsquid]

Hi Perla, thanks for your comment, it is a great question. It actually depends on how YOU (or the author of the plot) decide to represent the data, but usually YES, you would like to have upregulated genes (FC > 0) on the right, and downregulated genes (FC < 0) on the left. It's just more intuitive and easier to interpret.
But it's all relative. An example. You are comparing DEGs in liver cells versus neural cells. If genes on the right are UPREGULATED in liver cells versus neural cells, then it means they are DOWNREGULATED in neural cells versus liver cells. So it's always important to specify the groups you are comparing and which one is your 'base' or 'control' group. Hope this makes sense!

[@janelu3990]

9/3=2 ？

[@efrainm4649]

9/3 = 2???? Common dude.
You didn't even explain where does the p-value come from...

[@chrisp7336]

Very useful thanks