I have a human gene and I want to use in silico methods to study if it is regulated by some regulatory RNAs or by some DNA-binding proteins. What software, articles or databases would you recommend for this task?
One good resource, that I prefer, is the Ensembl database (Ensembl.org). You can search for your gene, I will use CA2 as an example:
http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000104267;r=8:85463852-85481493
Click on genomic coordinates link to the right of 'Location', taking you here:
http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000104267;r=8:85463852-85481493
Then in the 3rd window down (the largest), click the gear shape in the top left and look for the section on 'Regulation'. A tutorial of sorts should pop up for you. Turn on the regulatory feature tracks you would like to see and then click the check mark at the top right of this window. There is a huge amount of info available, so be prepared to spend some time both exploring and interpreting.
While there are a plethora of tools out there, it's hard to narrow it down to the best one. I would browse the Galaxy Project (www.usegalaxy.org). It is a workflow that integrates a large amount of bioinformatic tools into one platform. You may be able to find something there that will help you. I would also look into DECOD and using the NCBI database for regulatory RNA/DNA-binding protein motifs. Hope this helps.
TRED: a Transcriptional Regulatory Element Database (http://rulai.cshl.edu/TRED) was designed as a resource for functional studies and gene regulation studies.
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