GEO (Gene Expression Omnibus) is a gene expression data repository that accepts array- and sequence-based data. It is developed and maintained by NCBI (National Center for Biotechnology Information).

It has become very difficult to grasp the outline of data accepted by GEO, since they are very complex because of many Data units (such as Dataset, Sample, Platform) and variety of experimental methods.

To ease this situation, Dr. Okubo and colleagues at the National Institute of Genetics (Japan) have developed the “Gene Expression Omnibus (GEO) Overview”. It is now maintained by the Database Center for Life Science (DBCLS).

This tutorial describes how to use the “Gene Expression Omnibus (GEO) Overview”. It should be helpful to find out the outline of the abundant gene expression data available from GEO.

Click “Gene Expression Omnibus (GEO) Overview” linked from the LSDB home page.

The data sets accepted by GEO are categorized and organized by taxonomy (species type) and platform (methods or instruments used for gene expression profiling) tabs.

The number in parentheses shows the number of data sets available in a single category.

In this example, there are 8,099 data sets categorized under GeneChip.

For gene expression data obtained from animals, the samples are categorized by histology.

To sort the data sets by the title of a column, click the link.

The data sets can be sorted by ascending (light blue) / descending (light green) order. To switch between the sorting orders, click the title again.

The data sets can also be searched using the search box on the top right.

Type ‘hypoxia’ in the search box and click “Search”.

The search result displays 34 hits under the Human category and 39 hits under the GeneChip category.

Clicking one of the tabs will filter the results to the selected categories.

Click the tab labeled “Human”.

The results have been filtered to 1 data set related to hypoxia/Homo sapiens/SAGE NlaIII and 20 data sets related to hypoxia/Homo sapiens/GeneChip category.

From each hit data set, a link to the original entry at GEO is available.

Now let’s take a look at the entire data sets related with “hypoxia”.

Clicking “Overview” will display a table that organizes data sets by taxonomy (column) and platform (row).

Clicking one of the numbers in a cell will display data sets related with the selected taxonomy and platform.

For example, click “20” to look at the data sets that are related with “Homo sapiens” and “GeneChip”.

Data sets related with “Homo Sapiens” and “GeneChip” are shown.

Click “Top” and return to the front page. We will now look at the number of accepted data sets by GEO as a function of country.

Click “Countries”.

The numbers of accepted entries are displayed as a table and are also mapped on Google Maps.

Clicking one of the category tabs (in this example, “Plants”) will filter the data sets by the selected categories as seen earlier.

At the moment Japan appears to be in second place with respect to the number of plant data sets accepted by GEO.

Similarly, Japan is in 6th place with respect to the number of bacterial data sets accepted by GEO.

Clicking “All” and then “Transition” will display the changes in the number of entire data sets accepted by GEO.

The changes in the number of accepted data sets are shown as a line graph.

The y-axis plots the number of accepted data sets and the x-axis the time (year/month). Note that the y-values of each taxonomic division or platform type are not cumulative.

The top plot shows the changes in accepted data sets by taxonomy and the bottom plot shows the changes in accepted data sets by the kind of platforms used to measure gene expression.

Clicking one of the tabs will filter the data sets by the selected categories as seen earlier.

For example, clicking the “Plants” tab will display the changes in accepted plant data sets (top plot) and these changes broken down by the kind of platforms used (bottom plot).

Similarly, clicking the “Bacteria” tab will display the changes in accepted bacterial data sets (top plot) and these changes broken down by the kind of platforms used (bottom plot).