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modENCODE RNA-Seq data

Posted: Mon Jul 06, 2015 3:16 pm
by wleung
Question from Dr. Jamie Sanford, Ohio Northern University
I am doing some basic gene expression analysis on my gene of interest. Specifically, we are trying to determine which of the gene's isoforms are expressed in fly ovary. Is there a way to easily use the modENCODE data to find out isoform specific expression of a gene in a given tissue? I know on GBrowse you can see the developmental subsets expression data, but those are not tissue specific. I know there is a modMine, but I'm not sure I know how to use to ask what I want - which is simply "what isoforms did modENCODE detect in the ovary via the tissue specific RNAseq?"

Re: modENCODE RNA-Seq data

Posted: Mon Jul 06, 2015 3:30 pm
by wleung
I am unaware of an existing list from modENCODE that shows the isoform expression levels of each D. melanogaster gene.

I believe that all of the RNA-Seq information on FlyBase are summarized at the gene level (see the FlyBase RNA-Seq Release Notes). You can download the RPKM values for all the D. melanogaster genes through the "Precomputed data files" page at FlyBase (under "Genes" -> "RNA-Seq RPKM values").

FlyBase has just added a new feature (i.e. RNA-Seq by Region) in release 6.06 that shows the exonic expression data for each gene. You can access this tool either through the FlyBase home page or the Gene Report (available under "Expression Data" -> "High-Throughput Expression Data" -> "View exonic expression by tissue for <gene name>").

It is possible to use tools such as Cufflinks to estimate the expression level of each isoform in an RNA-Seq sample. Basically, after mapping the RNA-Seq reads against the D. melanogaster release 6 assembly (e.g., using TopHat), you can provide Cufflinks a reference annotation file and it will estimate the expression level of each isoform. The ovary-specific datasets are available through modMine under the DCC id numbers modENCODE_4244 and modENCODE_4266. The GTF reference file for D. melanogaster is available through FlyBase.

Depending on your research goals, you can use Cuffdiff and DESeq to identify isoforms that are differentially expressed in ovaries. Below are two papers that might be of interests: