TarBase identifies gene-targets through three identifiers, namely "HGNC_ID", "HGNC_Symbol", ENSGxxxxxxxxx", Which one of such identifiers is more reliable (unique) to extract the 3UTR sequences from Ensembl through BioMart function calls? What is the difference between "HGNC_ID" and "Entrez Gene ID" ? Whenever I look for such names I found described the story and reasons why such names exist and the agency which is in charge of assigning them ... but I am missing their usage and difference with other *to my eyes* similar identifiers. TarBase contains 1 miRNA called "Edited-miR-376a-5p". Could you please explain the meaning of this name and advice about the usage of such data ? Should I drop the "Edited-" substring and consider it as a regular Validated miRNA ? Thank you very much for your assistance and patience. Best regards, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Hi, On Tue, May 4, 2010 at 10:05 AM, <mauede at="" alice.it=""> wrote: > TarBase identifies gene-targets through three identifiers, namely "HGNC_ID", "HGNC_Symbol", ENSGxxxxxxxxx", > Which one of such ?identifiers is more reliable (unique) to extract the 3UTR sequences from Ensembl ?through BioMart > function calls? ENSGxxxxx stands for "Ensembl Gene ID", so if you're going to be using Ensembl, then I'd imagine that might be the best. One thing to note is that each gene can have several transcripts, identified by ENSTxxxxxx. Given that different transcripts can have different 3'UTRs, and that you're looking at miRNA-to-target interactions (that usually happen in 3'UTRs), there's another dimension you have to deal with. > What is the difference between "HGNC_ID" and "Entrez Gene ID" ? http://www.genenames.org/aboutHGNC.html > Whenever I look for such names I found described the story and reasons why such names exist > and the agency which is in charge of assigning them ... but I am missing their usage and difference with other > *to my eyes* similar identifiers. OK ... > TarBase contains 1 miRNA called "Edited-miR-376a-5p". Could you please explain the meaning of this name and advice about the usage of such data ? > Should I drop the "Edited-" substring and consider it as a regular Validated miRNA ? The first hit from a google search of "Edited-miR-376a-5p" will get you here: http://stke.sciencemag.org/cgi/content/full/sci;315/5815/1137 >From reading the abstract of that paper, I would imagine the "edited" part is actually quite important/relevant information. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Hi, Maura. On Tue, May 4, 2010 at 10:05 AM, <mauede@alice.it> wrote: > TarBase identifies gene-targets through three identifiers, namely > "HGNC_ID", "HGNC_Symbol", ENSGxxxxxxxxx", > Which one of such identifiers is more reliable (unique) to extract the > 3UTR sequences from Ensembl through BioMart > function calls? > Which gene id is from Ensembl? > What is the difference between "HGNC_ID" and "Entrez Gene ID" ? > Do you know about the HGNC database? If not, give that a google. > Whenever I look for such names I found described the story and reasons why > such names exist > and the agency which is in charge of assigning them ... but I am missing > their usage and difference with other > *to my eyes* similar identifiers. > > TarBase contains 1 miRNA called "Edited-miR-376a-5p". Could you please > explain the meaning of this name and advice about the usage of such data ? > Should I drop the "Edited-" substring and consider it as a regular > Validated miRNA ? > > A cool feature of the tarbase database is that it is searchable. I searched for this miRNA and then looked at the results. There is a paper that is linked. Follow that link and then read the paper. I hope that can answer your question. Sean [[alternative HTML version deleted]]