Downloading human age-related gene expression levels and making figures

Technical
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1

Hello:

I am new to using the Allen data. I am working on a project involving brain tumors. One type originates in younger patients and overexpresses developmentally related genes and the other type, which occurs in older patients, expresses genes more expressed in adult brain. When I look at the atlas, some of the genes have more than one horizontal bar graph on the same age scale. I am having difficulty interpreting the significance of this and downloading the data. The only thing I can do at this point is copy the color-coded horizontal bars. Can anyone comment on that, i.e., what do the lower bars represent? How do you download the data for a particular gene?

I can always make a simple Excel bar graph showing the differences of age-specific expression of genes of interest between the 2 tumor groups, or simply paste the color-coded bars together. Can anyone suggest something more sophisticated, for a good journal? I would be willing to take on a collaborator, if someone is particularly interested and skilled at making nice figures with this data, i.e., period and anatomic locations of expression.

Thanks,

Norm

2

Hi Norm,

For our RNA-seq atlases, there should only be a single horizontal bar per gene, unless you are looking at exon level expression (e.g., here); however, our microarray atlases often have multiple probes per gene (e.g., here). In cases with multiple probes per gene, each row represents expression of a different part of the gene, which often are highly correlated, but sometimes are not if the probes are measuring different isoforms of the same gene, or if one probe is “better” (for one of many biological or technical reasons). Finally, if you type in a gene with a rather generic name (e.g., MET, here), you can return a search with many different genes. In this case you’ll want to check the “Show exact matches only” box under the search bar.

For all of our microarray and RNA-seq data sets, there should be a link towards the bottom that says something like “Download this data”, which will allows you to download all of the data that is shown on the screen. Please be aware that the default heatmap in many of our atlases is a z score, and if you want the normalized intensity you will need to click on the color bar below the heatmap and change the units before downloading the data. The downloaded zip file will include an expression table, a table with information about the rows (genes) and a table with information about the columns (samples). You can also download all of the data for a given atlas in the relevant “Download” tab.

For visualization, we have the heatmaps for each of our atlases and a few other cool things that may be more challenging to find:

  • A heatmap overlaid on a sketch of the adult human brain (here)
  • A heatmap overlaid on a sketch of the developing human brain (here)
  • Fully interactive views of human and mouse cortical cell types
  • Isoform level expression of RNA-seq data in our Brainspan Atlas (here)
  • (If anyone notices visualizations I am missing, please reply to this post)

If none of these work, we would suggest downloading the data and making your own plot in Excel or some other program. For example, there are many R packages available for plotting and statistics of RNA-seq data. Please reply to this post if you have any additional questions.

Best,
Jeremy

3

Thanks so much Jeremy!
That was great.

Norm