miRNA target prediction tools tutorial | Targetscan | miRDB | RNA22|
Вставка
- Опубліковано 1 гру 2021
- This video lecture describes
1. What are different microRNA target prediction tools?
2. How to predict miRNA target genes using Targetscan ?
3. How to predict miRNA targets using miRDB?
4. How to perform custom prediction using miRDB
i.e. How to predict miRNA from target sequence using miRDB?
5. How to perform miRNA target prediction using RNA22 or RNA 22?
Links for microRNA target prediction tools
Targetscan:
www.targetscan.org/vert_80/
miRDB: www.mirdb.org/
RNA22
cm.jefferson.edu/rna22/Intera...
Video link to retrieve UTR sequeces from UCSC genome browser:
• 5' UTR, 3' UTR, CDS, P...
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For the easy to understand introductory lecture on microRNA ,Biogenesis, mechanism of regulation of genes by microRNAs, please watch this video. ua-cam.com/video/bibkF_7a2Yo/v-deo.html .
thanks for the greart content. I am a newbie phd student and I just started my project in miRNA field. This is very super helpful! cant thank u more.
Glad it was helpful! Wish you all the best for your Ph.D.
trust me you are the best.. i am really very thankful to u for making such an amazing informative video..please keep uploading such content
Thank you very much for your kind words. Please like and share the video and subscribe our channel to support us.
Excellent work as always ❤️
Thank you! Cheers!
It was very informative session for me. For my research, it will be very helpful.
Glad it was helpful. All the best with your research 😊
You are the best teacher
Thank you very much for your support.
thank you so much, it's very helpful. do you know how to combine results from those 3 website and make it into 1 diagram for comparasion? because i notice RNA22 only showed p value and not ranking like other 2, so i am curious how to combine them into 1 diagram like papers do. thank you
You are most welcome. If you want to find out the common miRNAs predicted by the three different tools, I would recommend using excel to find the common hits predicted by all three and then showing them in your paper.
Very helpful video Sir. I was stuck as I am beginner in this field of bioinformatics and your class has cleared all my doubts.
Thank you Sir. One more request, if you could upload a video on miRNA and lncRNA interaction, it will be very beneficial.
Thank you so much Ankur Banerjee. All the best with your studies. We will upload the video on miRNA and lncRNA interaction as soon as possible. Please watch this video on introductory lecture on miRNA ua-cam.com/video/bibkF_7a2Yo/v-deo.html
@@BiologyLectures Definitely sir. Thank you for your kind wishes and support.
@@ankurbanerjee4257 You are most welcome.
@@ankurbanerjee4257 Dear Ankur Banerjee, Please watch this video showing in silico lncRNA and miRNA interaction prediction. ua-cam.com/video/WBOQDFvuNJ4/v-deo.html
I have circRNA trancriptomic seq, how I can do circRNA-miRNA -mRNA network?
sir could you please tell about mirbase tool how to use
Sir keep up your good work
Thank you, I will
just subscribed. Please do one video using RNAHybrid, there is no video on this online analysis took
Thank you very much. Sure we will upload it as soon as possible 😊
The video was very helpful sir, I am using miRanda and RNA22 for target prediction. miRDB and Targetscan have limited to some species. Kindly suggest me a tool that uses miRNA and mRNA sequences as input for target prediction.
We would suggest to use miRDB.
How to find target miRNAs for plant speices? Any database other than PmiREN for plant species?
Dear Zunaira, Please find below the link for plant database: www.biosequencing.cn/TarDB
bioinformatics.cau.edu.cn/PMRD
mirvit.ipsp.cnr.it
How do we get the pre-miR sequence and design primers to make miR expression vectors?
Please use mirbase database. The link for which is below: www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MIMAT0000064
Thanks. Do we design primer on the sequence we get from this database or we add flanking regions for primer binding?
How to find out target miRNA for female sprague dawley rat ovary? induced by some chemical compound..
Please use google scholar to find the suitable article to serve your purpose.
sir, I am looking for website where I can put mutated UTR sequences and can see the interaction with mirna
Hi Rupa
Please use RNA22 for this purpose. Basically put your mutated utr sequence and microrna sequence. You will be able to see if there is any interaction. You can also use mirdb.
Sir ,question please, for detecting novel miRNA and novel lncRNA ,what is the most common method used ?can RT-PCR be used for such things??
Detecting novel miRNAs and lncRNAs can be done using a variety of methods, including RNA sequencing (RNA-seq), microarray analysis, and qPCR-based approaches.
RNA sequencing is a powerful tool for identifying novel miRNAs and lncRNAs, as it allows for the detection of transcripts without prior knowledge of their sequence. This method involves sequencing RNA from a sample of interest and comparing it to a reference genome or transcriptome. The resulting data can be used to identify novel transcripts, including miRNAs and lncRNAs.
Microarray analysis can also be used to detect novel miRNAs and lncRNAs, although this method is not as sensitive as RNA-seq. Microarray analysis involves hybridizing labeled RNA from a sample of interest to a microarray chip containing probes for known miRNAs and lncRNAs. Novel transcripts can be identified by analyzing the hybridization patterns of the labeled RNA.
qPCR-based approaches can also be used to validate the expression of novel miRNAs and lncRNAs identified using RNA-seq or microarray analysis. However, qPCR is not typically used for initial discovery of novel transcripts due to the need for prior knowledge of the target sequence.
In summary, while RT-PCR can be used to validate the expression of novel miRNAs and lncRNAs, RNA sequencing and microarray analysis are more commonly used for initial discovery of novel transcripts.
@@BiologyLectures thanks very much sir
@@ego9086 You are most welcome.
Sir, how to get the 3' UTR sequence ? Please guide me
Dear Rashmi
Please find below the link for the video where we have described how one can get 3 UTR sequences ua-cam.com/video/Bn2IGYLsQLQ/v-deo.html
Hello I am doing miRNA regulation of a gene. Can you guide me
Please watch this video ua-cam.com/video/bibkF_7a2Yo/v-deo.html
may i know how to download mirDB search result?
We would recommend copying and pasting the results of miRDB in excel.
I subscribe
Thank you very much for your support.
sir how to get plant mirna sequences?
To get plant miRNA sequences, please use the following database
pmiren.com/
And to find out if miRNA and your gene of interest are interacting, you can use the RNA22 tool as described in the video.
@@BiologyLectures sir my plant of interest beta vulgaris is not in pmiren ...then what will i do?
@@Piyalimukh03 Please go through this paper, maybe this will help
bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-83#:~:text=MicroRNAs%20%28miRNAs%29%20are%20endogenously%20encoded%20small%20RNAs%20that,the%20model%20food%20legume%20Phaseolus%20vulgaris%20%28common%20bean%29.
@@Piyalimukh03 Also please go check these databases:
www.biosequencing.cn/TarDB
bioinformatics.cau.edu.cn/PMRD
mirvit.ipsp.cnr.it
@@BiologyLectures ok sir