Hub Genes Identification | Bioinformatics | Complete Practicle Tutorial | Urdu | Hindi
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- Опубликовано: 11 сен 2024
- 🎥 This video demonstrates the identification of HUB genes from a complex gene network. By watching this video, you'll learn how to analyze a microarray dataset using GEO2R analysis and identify differentially expressed genes (DEGs). Additionally, you'll be able to use the DEGs to build a complex interactive network and further analyze it to identify your HUB genes using Cytoscape software. 🔬🧬
#bioinformatics #drnajeeblectures #computationalbiology
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DEGs identification through GEO tool ka tutorial dydain.
ruclips.net/video/pQd-KimSxtM/видео.html
Can you tell how you get past papers of general subject or how you scored 78?
I watched all the videos that were basically about the past papers. Follow youtube channels (Mujahid academy, GAT academy, Technically explained and Aspirants of Future). These will help you alot...
JazakAllah
DEG identification through Cytoscape tutorial
Facing error while uploading table file
“No rows copied ! ! Check that key column for network matches imported key column”
Vary good explanation
Thanks and welcome
Please make a full tutorial on cytoscape
ok...
Agr mara pas aik pathway ma mutations ha e.g RAAS pathway ma. Uski hub genes kaisy bna skty hain?
Well if its a single pathway (RAAS) so visualize it on kegg pathway database and see which gene has the most connections...that would be your hub node.
OR
copy all the concerned genes, paste it in string, move it to cytoscape and apply cytohubba
OR there must be a way to upload a kegg pathway to cytoscape where than apply the cytohubba and find the hub gene. Thanks
Can u tell me that how we find the upregulated and downregulated genesin the cytoscape ?
Well i planning to make a video over it but in order to save your time follow the link below...
ruclips.net/video/1l0tIHrEezg/видео.htmlsi=KVMrCZFBqtpXFkxQ
Can you share same method for key mirna identification
Well as per my existing knowledge, mirna can omly be retrieved after performing RNAseq analysis...You can choose existiing known mirna sequences and match your reads with it...Thanks
How can we find upregulated and downrrgulated genes in network through log value
higher the log value higher will be the expression of the genes and vice versa...GEO2R analysis is the most easy way to find the expression...Thanks
upregulated or downregulated pr ayk banaien
In sha Allah....share your complete query...this will help me to organize a tutorial
what if we dont get gene symbols and ids in output file from geo2r
i got gene sequence
so i got error in stting as they need protein data
No problem brother, just perform blastp of your sequence in NCBI and select the top most aligned sequence. You can also insert your sequence directly in NCBI search box and you will get your protein name and symbol...Thanks
@@scienceforeveryone8827 what if fc value has not downloaded or not shown in table options
Watch this video...It might help...
ruclips.net/video/HH3Mll4W5WE/видео.html
P.adj pa filter k bad ..log fc pa .filter work ni krta ..and again full table show hta ..up and downregulated genes ni .
Thanks for watching...lagFc value only shows the up regulated and downregulated genes there is no such filter approach for it (up to my knowledge)...The real filtration is to be applied for the adjusted P-value because it filter out the black genes from the red and blue (see volcano plot in the video)
First apply the adjusted P-value filter...it will filter out the DEGs and than sort the LogFc column of the genes from ascending to decending order...upregulated genes (logFc > 0) and down regulates (logFc < 0)...
Hope you get it...
There is no Geo2r button in my interested data set. How to proceed i am beginner please help
Well well...now here is the main twist...There is no GEO2R option with all the datsets...You will than proceed with your data using R programming language. I am working on it and I will soon upload the tutorial in detail as soon I learn it completely...This will not take that much time just stay tuned to my channel. I am advising that if you are working with such datasets so start learning R programming. Thanks
@@scienceforeveryone8827 okk.. thanks for your support
How we contact you
You can mail me (nadeemkhanf577977@gmail.com)
DEGs identification through Cytoscape and MCODE use krny ka tutorial dydain please.
Thanks for watching the video...Yet I am busy in composing videos related to In-silico vaccine designing and it might take a couple of weeks to complete that series so I find a tutotrial video that will help you instantly...
Click on the link attached below and u will find a solution to your queries In sha Allah
ruclips.net/video/1l0tIHrEezg/видео.html
If you still have queries, than let me know...THANKS
What if we get the transcript_cluster ids in the file and no gene symbols
The entire information about the probes used in the microarray experiment is stored in GPL file that is provided by the designer. Each probes correspond to a specific sequence in the GPL table. Match the probe of your missing gene with the sequence, go to NCBI blast and pick the top alligned sequence that will lead you to your gene symbol. Thanks