Entering edit mode
7.2 years ago
syedahira1
•
0
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??
I think you should elaborate more your question. What kind of data you have?
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
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.
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 ?
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
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!)