Question: searching a method for analyzing Differential Expressed Genes instead of constructing regulatory network
0
gravatar for syedahira1
2.1 years ago by
syedahira10
syedahira10 wrote:

instead of gene regulatory networks what else can i perform in identification of deregulated gene in myositis based on bioinformatics analysis? can you please help me??

gene • 666 views
ADD COMMENTlink written 2.1 years ago by syedahira10
1

I think you should elaborate more your question. What kind of data you have?

ADD REPLYlink written 2.1 years ago by lessismore710

I have retrieve a expression data-sets which were retrieve by GEO database and then using limma R package i have identified total of 378 DEGs, including 202 up- and 176 down-regulated genes, in synovial tissues of RA patients compared with healthy controls what i am trying to ask is that i have perform different analysis steps on these DEGs like 1-Functional annotation of DEGs 2-Protein–protein interaction network and I am trying to find some other new bioinformatic steps that can be applied on these DEGs except the construction of transcription regulatory network i hope you get my question thank you

ADD REPLYlink written 2.1 years ago by syedahira10
1

I am not an expert in that, but i think that you should address a biological question. Given that it is an autoimmune and chronic disease, you could compare your results (in term of DEGs and PPI) with the results of other studies which involved the same disease (in the same or other stages), or other autoimmune and chronic diseases to search for a specific pattern. You could also compare your results in terms of gender (women and men) and age (young and adults). You could maybe search for variants in your genes, or, if you have this information, investigate a familial predisposition for that.

ADD REPLYlink written 2.1 years ago by lessismore710

Data analysis is best done to answer a question. What kind of data do you have and what question are you trying to address with it ?

ADD REPLYlink written 2.1 years ago by Jean-Karim Heriche21k

I have retrieve a expression data-sets which were retrieve by GEO database and then using limma R package i have identified total of 378 DEGs, including 202 up- and 176 down-regulated genes, in synovial tissues of RA patients compared with healthy controls what i am trying to ask is that i have perform different analysis steps on these DEGs like 1-Functional annotation of DEGs 2-Protein–protein interaction network and I am trying to find some other new bioinformatic steps that can be applied on these DEGs except the construction of transcription regulatory network i hope you get my question thank you

ADD REPLYlink written 2.1 years ago by syedahira10
1

I think it was expected to get your hypothesis statement after J-KH's comment in order to help you find the right tool to use to test your hypothesis. So, again, what is your hypothesis statement (if you even have one!)

ADD REPLYlink written 2.1 years ago by theobroma221.1k
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