Retrieval of Gene Expression Profile or DataSets from NCBI GEO
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- čas přidán 21. 04. 2019
- Tutorial for retrieval of gene expression profiles or datasets from National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database.
NCBI GEO: www.ncbi.nlm.nih.gov/geo/
NCBI GEO Entries: www.ncbi.nlm.nih.gov/geo/info...
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Very informative videos!
Love you videos.
Can you please make a video on differential gene expression analysis from TCGA using R.
Sure. I'll post soon.
Thank u a lot. Finally I found!
You're welcome!
Thank you Ashok
You're welcome!
How to get the P-vale and logFC value for dataset from GEO also how to identify the differential expressed gene ?
Use GEO2R site www.ncbi.nlm.nih.gov/geo/geo2r/
Sir
In ncbi forms to get the accession number, there is column for reference author. What to write there?
Reference author means the 'name' of the data submitter.
@@AKBIT thanks sir!
What to write in?
FORWARD PRIMER NAME
REVERSE PRIMER NAME
Sequence Author
Isolation source
Isolation place
Can you mention the timeline in the video where you have doubt?
Hello Sir,
Thank you for sharing this video. Very useful. I am working a little bit sane concept. Up to this, I understood how to download the RNA-Seq dataset using NCBI-GEO. But after this how-to align this data? I have to differentiate between a common splicing site and an alternative splicing site. Please suggest me.
Sorry for the late response. GEO2R is the build-in gene expression data analysis (based on R language) tool. I'll post a video on it soon.
www.ncbi.nlm.nih.gov/geo/geo2r/
@@AKBIT Sir,
I have one query on how I can differentiate between a common splicing site and an alternative splicing site. Which data from NCBI do I have to use Transcript data of a particular gene or any other data? After that, I have to align that data. Please suggest me.
@@namratajawanjal9549 You can download a common splicing site or alternative splicing site from NCBI-GEO, but it must be relevant to your research. The NCBI-GEO supports data analysis through GEO2R with a specific dataset or profiles only. Aligning the RNA-seq dataset can be done through many software. Galaxy is a commonly used cloud server that consists of many alignment tools for RNA-seq data analysis.
@@namratajawanjal9549 Refer this article it will be useful to you www.ncbi.nlm.nih.gov/pmc/articles/PMC5476949/
Select a raw data set of Arabidopsis thaliana from GEO. Put it into GALAXY and de-contaminate it. After filtering you are supposed to align it on the any of the prescribed reference and show the results
Tell me plz how i do
Your question is not clear to understand.
from GSE68465 I want to delete GSMXXXX samples which are related to dead patients and normal patients. How do I delete. Can you help me in solving this query for my research.
You cannot delete or modify datasets stored in the database. If you want to ignore GSMXXXX samples which are related to dead patients and normal patients, you must select samples (CTRL + Left click the hits for multiple selection) and assign group name(s). Now, you can analyze the selected samples (group) alone. For brief explanation, watch this video czcams.com/video/EUPmGWS8ik0/video.html
Why you select the lower value in in Sample Rank ?
Lower rank represents higher accuracy. Rank is similar to grading system.
What software/app do you use to download soft files?
You can directly download using browser itself.
@@AKBIT i cant download file ,
@@backtesting12 0:55 Watch at this timeline to download the dataset. NCBI have temporarily restricted to download some datasets through FTP. It may possibly be removed from the NCBI server.
Hi, hope you're doing well
My major is statistics and unfortunately i know almost nothing about genetics...
But i have to do some analyses on them.
I have two questions, would you please help me?
1) We have 100 people, for each of them we measure their genotypes.
I wanna know that are these genes have features?
If i want to explain about what i mean by features, i should say that for example for each atom , say oxygen, we have specific number of protons, electrons and .... but among chemical which has oxygen, there are different number of oxygen...
So features means something that is fix.
Now I wanna know that do we have features for each gene?(something that is fixed and not change for different people, genotypes are changed among different people)
2) if the answer of above question is yes(we have genotypes for each pesron,they are changing from one person to another, and we have features for each genes), how can i have data like this?
I'll be very thankful if you help me...
Thanks in advance.
Genetics is a vast area to explain. According to your query, I'll explain simply. All living organisms have feature. In physical aspect, you can consider body parts/organs which are common - but varies like tall, short, fat, etc. In biological aspect, genetic memory, genetic disorders, etc. - but varies over evolution due to genetic crossover (father & mother).
Thank You. But it would be better if you either say or write the instruction in the video
Thank you for your feedback. I will follow in future video making.
Sir, could you add voice explanation for this video. I'm an undergrad. I find it difficult to understand what's going on
Sorry for the inconvenience. In future videos the problem will be rectified. If you have any queries, send mail to ashok.bioinformatics@gmail.com
Hello sir!How to contact you please?
ashok.bioinformatics@gmail.com