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

Biostatsquid
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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.scienc...
And here is a nice, short explanation on how to interpret volcano plots:
www.htgmolecul...

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8 сен 2024

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Комментарии : 70   
@mohamedirfan5480
@mohamedirfan5480 Год назад
Keep making videos ma'am. This is the future of biotechnology. You are a saviour. God bless this channel!!
@nathanieldanielrabo2423
@nathanieldanielrabo2423 Месяц назад
Exceptional. Thanks 🎉
@AbhishekVerma-xw3lz
@AbhishekVerma-xw3lz 8 месяцев назад
3:16 The value of gene expression in B should be 6 instead of 9. On a side note, the video provides good explanation.
@sanariaaljaf9619
@sanariaaljaf9619 3 месяца назад
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.
@AzminaAlisa
@AzminaAlisa Год назад
Easy and simple to understand! Thank you so much for your comprehensive guidance!
@janahanke5420
@janahanke5420 9 месяцев назад
this video saved me... my assignment would have been a fail otherwise, thank you so much!!
@AyrodsGamgam
@AyrodsGamgam Год назад
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.
@biorainbows4313
@biorainbows4313 Год назад
What a great explanation! Thank you so very much :)
@spalding5198
@spalding5198 11 месяцев назад
You don’t know just how happy you’ve made me! Thanks immensely for what you do!!!
@trixstandflipped
@trixstandflipped 7 месяцев назад
Fantastic video explained in simple yet very applicable terms. Thank you!
@odothomas1851
@odothomas1851 2 месяца назад
Amazing. Thank you
@JorgeCastillo-ko3im
@JorgeCastillo-ko3im Год назад
Very well explained. Easy to understand. Thank you.
@biostatsquid
@biostatsquid Год назад
Thank you! I'm glad it was useful:)
@raha1603
@raha1603 6 месяцев назад
As usual, it is very clearly explained and yet very informative, thanks.
@DarkBumbelsztein
@DarkBumbelsztein Год назад
this video was so clear and so nice!!! thanks so much. PCA plots next, please!! a super lost Metabolomics student here
@biostatsquid
@biostatsquid Год назад
Hi Julia thank you very much, this means a lot! PCA plots definitely on the list;)
@asmaal-yousofi3165
@asmaal-yousofi3165 4 месяца назад
Very useful thanks
@alejandrotorres8586
@alejandrotorres8586 Год назад
Excellent explanation. Greetings from Mexico
@kiplimosimon1429
@kiplimosimon1429 4 месяца назад
I enjoyed the explanation. it is very clear. Thanks so much
@MrAseem777
@MrAseem777 9 месяцев назад
Precise and clear..great effort.. waiting for such useful videos
@nami17
@nami17 Год назад
This was really helpful! Thank you :)
@vinton1881
@vinton1881 Год назад
Clear explanation! Thank you
@nehapimpalwar7339
@nehapimpalwar7339 3 месяца назад
VERY INFORMATIVE VIDEO, THANKS A LOT IT MADE MY LIFR EASIER
@sumalatha1263
@sumalatha1263 23 дня назад
Useful thanx
@debojittalukdar5196
@debojittalukdar5196 Год назад
Extremely Good and helpful video....I need more videos on MA plot, PCA plot, Kegg ,Bubble plot and Heat Map Analysis..Please .
@matheusalmeida773
@matheusalmeida773 10 месяцев назад
Fantastic explanation! Thank you very much!
@parsaarabshahi6600
@parsaarabshahi6600 4 месяца назад
very useful thank you!
@biostatsquid
@biostatsquid 4 месяца назад
Glad it was helpful!
@manjinderkaur-hf5pb
@manjinderkaur-hf5pb 4 месяца назад
Very useful
@zahraaalawadly8583
@zahraaalawadly8583 7 месяцев назад
The video is really so useful. Thank you!
@maheshrani6609
@maheshrani6609 Год назад
well explained....simple but very effective.
@ruthgyereh1052
@ruthgyereh1052 Год назад
More than useful. You’re a star
@MHiol1
@MHiol1 10 месяцев назад
Thank you.
@kibuasmr4423
@kibuasmr4423 Год назад
Awesome vid, thanks !
@MsFireroll
@MsFireroll Год назад
Very great ! But 9/3=2 ????
@domi1096
@domi1096 Год назад
I was wondering the same...
@AyrodsGamgam
@AyrodsGamgam Год назад
just a typo, she meant 6/2
@gopalkalwan7465
@gopalkalwan7465 10 месяцев назад
6/2 should be there because the purpose was to get 2 fold
@muttugoudr2346
@muttugoudr2346 8 месяцев назад
thank you!
@martagarcia1946
@martagarcia1946 Год назад
Amazing explanation! Thank you very much! Love all your videos, I can understand everything! :)
@sanjaisrao484
@sanjaisrao484 Год назад
exellent thanks
@nasserbenomar
@nasserbenomar 7 месяцев назад
thank you so much
@mobeenshaik9164
@mobeenshaik9164 7 месяцев назад
keep on doing this beautiful work
@user-so6qc3gd5o
@user-so6qc3gd5o 7 месяцев назад
That was incredible thank you :)
@partha_plethorapedia
@partha_plethorapedia 6 месяцев назад
very nice explanation...thank you.
@rayees.ahamed
@rayees.ahamed 7 месяцев назад
Well explained. Thank you.
@lucianosouza6766
@lucianosouza6766 9 месяцев назад
it is a well done video. Thank you so much ;)
@koustavroy350
@koustavroy350 Год назад
Very clear presentation
@lamaismaiel9870
@lamaismaiel9870 Год назад
It is very nice and well-explained, thanks!
@user-if2di8gh1o
@user-if2di8gh1o 6 месяцев назад
amazing. thank u biostats squid
@rabeeakhan563
@rabeeakhan563 8 месяцев назад
please make videos using multiple bioinformatics tools to interpret RNA seq data.
@biostatsquid
@biostatsquid 8 месяцев назад
Thanks for your suggestion! Will definitely do:)
@dr.tranngocthien
@dr.tranngocthien Год назад
thank you
@anujvermabiotech
@anujvermabiotech 5 месяцев назад
Thanks
@nidhisingh7066
@nidhisingh7066 Год назад
you explained this in a very nice way!!
@biostatsquid
@biostatsquid Год назад
Thank you Nidhi! Glad it helped:)
@Claireshoon
@Claireshoon Год назад
That's really clear and thank you: please next OPLS-DA
@biostatsquid
@biostatsquid Год назад
Glad you found it useful Shoon! And thanks for your suggestion, I will definitely add it to the list:)
@folenspill
@folenspill 2 месяца назад
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
@biostatsquid 2 месяца назад
Yes, apologies, that was a typo! You are correct:)
@daniiujes9577
@daniiujes9577 Год назад
What a video
@user-io6wu9px2n
@user-io6wu9px2n Год назад
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
@biostatsquid Год назад
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
@user-io6wu9px2n Год назад
thank u @@biostatsquid
@PerlaAlejandra009
@PerlaAlejandra009 Год назад
Always the side right is where are upregulating genes and the downregulated genes are in left side?
@biostatsquid
@biostatsquid Год назад
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
@janelu3990 Год назад
9/3=2 ?
@efrainm4649
@efrainm4649 Год назад
9/3 = 2???? Common dude. You didn't even explain where does the p-value come from...
@chrisp7336
@chrisp7336 Год назад
Very useful thanks
@shabihaheea39
@shabihaheea39 Год назад
Very helpful
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