General suggestions regarding gene expression
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@mariagiovannetti86-12375
Last seen 4.6 years ago

Hello everyone,

I'm Maria and I've just joined this amazing community to start learning basics that are mainly related to my future PhD topic.

The aim of my doctoral studies, in fact, is to find out all the genes that are coexpressed and repressed with the expression of a specific gene.

Which are the first steps am I supposed to take?

(my level of experience with r is "beginner" i should say)

thanks in advance,

M

geneexpression • 621 views
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@gordon-smyth
Last seen 32 minutes ago
WEHI, Melbourne, Australia

Well, the first steps don't involve R, but do involve you and your supervisor.

If you are biologist, then you need to plan some gene expression experiments. RNA-seq is normally the technology of choice these days.

If you are a bioinformatician, then you need to explore what data is relevant that you want to analyse. For example you might explore the gene expression omnibus (GEO) repository at the NCBI that contains many thousands of microarray and RNA-seq datasets.

If you have a specific experiment or dataset, then people here on Bioconductor could give some advice on how to analyse it. Correlating the expression of one gene with others is quite easy once you know how to do a differential expression analysis.

And of course, even before finding data, you should be doing some sort of literature review.

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Thanks a lot Professor Smyth,

actually I'm trying to "surprise" my supervisor and I would love to start acquiring this expertise (or basically trying to do that with a "learning-by-doing" approach) since there's time ahead. I'm an immunologist (or basically my background is in immunology) but the PhD will use a bioninformatic approach even though it's a PhD in immunology. so, trying to follow your advice, I may mine dta in GEO so trying to practice a bit.
Do you have any suggestions about what kind of experiment could be useful to start? maybe some explained ones?

Thanks a lot.

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If you were my student, I would want to be consulted rather than surprised. And I would probably advise you to collaborate with a bioinformatician and to concentrate your own time on the immunological science rather than trying to be a part-time bioinformatician yourself.

If you are simply trying to gain some familiarity with R, you could start with the R introduction:

  https://cran.r-project.org/doc/manuals/r-release/R-intro.pdf

Note that Bioconductor is not the place for tutorials on R though.

Once you know something about R, you could work through a case study RNA-seq analysis, for example:

  https://f1000research.com/articles/5-1438/v2

However be careful that time spent on Bioconductor is not just "busy" time avoiding your real topic. I work with many immunology PhD students, and IMO your primary task at this early stage should be to understand the science that your supervisor wants you to work on. It would be a good idea to write to your proposed supervisor to ask for advice on what he or she thinks you should be reading or studying.

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