How Do I Annotate Rna-Seq Count Tables That Were Processed Via Star->Htseq-Count Using Illumina Igenomes Ucsc Hg19?

Question

[ndejay]

Hi,

I am new to NGS data processing world. I performed read mapping with STAR and counting with HTSeq-Count using the GTF and chromosome files provided by the TopHat/Cufflinks group (modified Illumina iGenomes UCSC hg19 as found on http://cufflinks.cbcb.umd.edu/igenomes.html). I am now analyzing their contents using differential expression analysis R software (DESeq). The data frame I currently have has samples as columns and gene names (identical to those that are on the GeneCards annotation database, I believe) but I would like to annotate them further in R. Is there a way to do this? Here is an example of what I have:

             XXXX0001      XXXX0002
A1BG       202.900518  3.744657e+01
A1BG-AS1   210.380899  19.96663e+01
A1CF         6.422366  9.354143e-01
A2M        112.642157  5.831635e+04

And I want to be able to retrieve information regarding each gene (e.g. A1BG -> Alpha-1-B Glycoprotein), as seen in http://www.genecards.org/cgi-bin/carddisp.pl?gene=A1BG. My guess is that as soon as I can determine what annotation convention these gene names follow, I should be able to easily convert between nomenclature (Entrez, HGNC, etc.) How do I go about breaking the ice?

Do let me know if I omitted any relevant information and thanks in advance.

[Irsan]

Follow a bioconductor annotation tutorial and you will know :-) look at the Org.hs.eg.db package. You want to convert gene symbols (A1BG) to gene names (Alpha-1-B Glycoprotein)

[ndejay]

You are correct! I absolutely overlooked that! Thank you very much @Irsan @SeanDavis

Answer 1

[Sean Davis]

Your gene names appear to be HGNC symbols. From there, you could use the org.Hs.eg.db package (as suggested by Irsan above) or biomaRt.