Field of Science

Learning to use the NCBI Gene Expression Omnibus

As part of our workup for the toxin/antitoxin manuscript, I want to find expression data for the homologs of the Haemophilus influenzae toxin and antitoxin genes.  The former post-doc recommends that I use NCBI's Gene Expression Omnibus ('GEO') for this.

I'll need to learn how to search the GEO for specific accession data and data from specific taxa.

I'll also need to find out the specific identifiers for the genes I'm interested in, in the species I'm interested in.  I think I can use BLAST searches (queried with the H. influenzae sequences) to find the species and links to the DNA sequences of the homologs, and then I can look at the gene records to find the strain and gene identifiers.

Then I need to check if anyone has reported doing gene-expression studies on this strain or species (ideally the same strain, but I think/hope the gene identifiers will be consistent across strains).  These reports should contain the GEO accession numbers for the data.

Then I can ask GEO for the data for this study.  But I don't know what format the data will be in, nor how hard it will be to find the information about the genes I'm interested in.

The best situation would be if GEO has done its own analysis on the data and made this available as a curated 'GEO Dataset' or a 'GEO Profile'.  I could then search the GEO Profile to see their analysis of the particular genes I want to learn about.

Here's a phylogenetic tree showing the relationships between the concatenated toxin/antitoxin sequences in the species they're found in.  (I should also have a tree showing the relationships of the species themselves, but I haven't drawn that yet.)



So I'll start by searching BLAST with the amino acid sequence of HI0660, the H. influenzae toxin, and limiting the search to Streptococcus species.  Because I want to find the genes, not the genomes, I'll do a BLASTP search against Streptococcus protein sequences in the database.  OK, this gets me species and accession numbers for the (mostly 'hypothetical') proteins, but not usually strain identifiers or gene names.  

Will I be able to use a gene accession number to search GEO?  Apparently yes!



Now let's try searching GEO for the gene accession number of a gene I'm sure it has in at least one Profile:  The H. influenzae CRP gene:


But GEO does find it if I search for it by its gene name: 'HI0957'.  


I think the red bars are expression levels in the six samples of the study.  Yes, and clicking on them gets me the actual data from the study.  Now I can see the Y-axis and discover that, although the red bars look dramatically different, the differences are actually quite small (range 6300-6300).



So this control search tells me that I need to know gene names (or whatever identifiers are being used) for the genes whose expression I want to learn about.  Hmmm...  I wonder if GEO provides any help for this issue.

I also tried starting with a TBLASTN search, which will get me the position in the genome where the homolog is encoded.  I can then look at the genome sequence, find the position, and see if the gene has a name.  The Streptococcus pneumoniae homolog of HI0660 (the H. influenzae toxin) is SP_1143, but searching GEO for this finds nothing

2 comments:

  1. I think you can call the attention of the webmaster for ncbi GEO. I didn't last 5 mins on the site because it is kinda complex.

    ReplyDelete
  2. I think you can call the attention of the webmaster for ncbi GEO. I didn't last 5 mins on the site because it is kinda complex.

    ReplyDelete

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