Need help looking for datasets about the transcriptional regulation of a gene
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3.1 years ago

Hello, I'm a student just starting research, and I'm looking for datasets about the transcriptional regulation of HDDC3, nothing came out of the search in GEO datasets and EBI, but there were results such as "HDDC3 - p63 depletion effect" [1] when I searched for "transcriptional regulation of HDDC3" in GEO profiles. The problem is that when I click the GEO datasets link of these results, I get these studies that seem to have nothing to do with the transcriptional regulation of HDDC3 (or at least not to my knowledge.) Is this the right way to find datasets? If it is, how can I know which datasets or perturbation have the most altered HDDC3 mRNAs?

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As you start your research, you should spend quite some quality time on reading the literature around that gene. Are there known regulators, inhibitors or modifiers associated with that gene? If so, you can check for datasets such as mRNA-seq on cells that received a suitable treatment, e.g. with an inhibitor, or have a knockdown/out or overexpression of a known regulator. Is there anything already known about this gene?

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Actually, I'm a second-year student in university, this is part of my assignment, and unfortunately has nothing to do with my project. Our teacher gave us this assignment after a brief introduction into data analysis:

Dr. X is trying to understand the transcriptional regulation of HDDC3. Dr. X chooses to employ the publically available data base of GEO (http://www.ncbi.nlm.nih.gov/geo/) and EBI (https://www.ebi.ac.uk/gxa/home).

  1. Among all the datasets, can you pick 3 datasets and perturbation by which HDDC3 mRNAs are altered most (either direction is fine)
  2. Can you download all the .cel file, RMA normalize the array data and obtain the relative expression of HDDC3 mRNA levels ? For those of you using Mac, you can get the help from your classmates with Expression Console on PC ?
  3. Can you perform the GSEA to compare the pathway enrichment vs. depletion in the treatment vs. control samples ? One short paragraph describing your results on the expected and unexpected changes in pathways.

I've discussed with my other classmates, but none of us have been able to find any datasets yet, that's why I came here for help. Is it possible that you can give us some hints? I must admit that I'm not really sure that I understand the questions, and I'm completely stuck, I would really appreciate some hints. Thank you very much.

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I undeleted this thread, please do not delete post after they received helpful comments, this would be antisocial towards people who are willing to help. You should be ok to frankly admit that you needed a little hint in the right direction.

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3.1 years ago

Search for the gene in GXA, go to differential expression, sort by fold change and download the top three. Seems fairly simple to me.

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Thank you sooo much!

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It is very nice that you are expressing your gratitude, but deleting your content is not the way Q&A is supposed to work.

Cheers, Michael

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3.1 years ago

Hint: For GEO you can use Geoprofiles. Navigate to the Geoprofiles page and enter a gene name, see what comes out.

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