HEY,

I am looking for any package in R provides me a list of micro RNAs for a differentialy expressed genes usng different databases.

i have list of 48 candidate genes identified for a specific disease and now i am looking for micro RNA for these geens.

anybody help me... i found many ways to get information about genes through micr RNA data but not finding any approach to get micro RNA information through genes datA

Hi,

What organism are you working with? When you say "using different databases", do you already know what databases to use for your organism or do you expect the R package to figure this out for you? Have you tried to lookup your genes on the UCSC Genome Browser? People in your situation generally know where to find the annotations for their organism. This already makes a big difference. The typical situation is that they have access to a GFF or GTF file that contains the information they're interested in. If you have access to such file, then import it in R with import() (from the rtracklayer package) or makeTxDbFromGFF() (from the GenomicFeatures package). The former will return you a GRanges object and the latter a TxDb object. Choosing one or the other depends on what you want to do downstream. See ?GRanges (in the GenomicRanges package) and ?TxDb (in the GenomicFeatures package) to learn more about these objects. If you choose the latter, you might consider calling transcripts(txdb, columns=c("tx_name", "tx_type", "gene_id")) on your TxDb object. This will return a GRanges object containing all the known transcripts for your organism. The tx_type and gene_id metadata columns will contain the type of transcript (hopefully some of them will be micro RNAs) and corresponding gene id, respectively. See ?transcripts for more information.

H.