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Uploading Probe IDs

To upload a list of probe IDs (with or without expression values), select the expression platform (say AFFYMETRIX_MOE430A_2) in the “Add Data Sets” pane and select the option “Upload Probe List”. Browse to the CSV (Comma Separated Value) file containing the probe IDs and click “GO”. Click here to understand more about the probe IDs file format.

Retrieving whole platform Gene IDs

To retrieve a list of Gene IDs represented by an expression platform, select the expression platform (say AFFYMETRIX_MOE430A_2) in the “Add Data Sets” pane and select the option “Get all Gene IDs”. Click on “GO”.

Using biological filters

Once a list of Entrez Gene IDs has been obtained either by mapping uploaded platform-specific probe IDs or retrieval of whole platform Gene IDs, the user has the option of applying ExpressO’s inbuilt biological filters to generate gene sets that may be biologically significant to their hypotheses. For example, the biological filter “Growth Factors (Human)” is a list of human growth factor genes derived from the Gene Ontology term “growth factor activity” and all its child terms. The entire list of genes (and their annotations) in the filter may be viewed by clicking on “View all genes in this filter set”. After clicking on “Apply Filter”, ExpressO will return a list of genes that are both part of the current list and the list in the selected biological filter. If there is no intention to apply any biological filter to the current list, the user may ignore this functionality and proceed to saving the list as a data set.

Saving data sets

A list of Entrez Gene IDs that has been obtained via the following methods may be saved as a data set:

• Mapping uploaded platform-specific probe IDs
• Retrieval of whole platform Gene IDs
• Application of a biological filter
• Selection of section(s) within a data sets comparison Venn diagram

To save a data set, the user has to key in a data set name and description before clicking on “Save”.

Comparing data sets

Comparisons between data sets can be performed at the “Compare Data Sets” pane. To compare data sets that were derived from the same species, the user will have to select the data sets (in this case the data sets “MOE430A_2” and “MOUSEREF_8” were chosen), choose the type of display (Venn diagram or bar chart) and click “Submit Query”.

The following figure shows the comparison output by ExpressO in terms of a Venn diagram. The user can select one or more sections within the Venn diagram by clicking on the number of genes (in this case, the 11734 overlapping genes have been selected) and click on “Display Section Genes” to view the list of Gene IDs and their annotations. Thereafter, the list can be saved as a data set for future analysis.



The following figure shows the comparison output by ExpressO in terms of a bar chart. This form of display is particularly useful for time series data (for example, microarray data of embryonic stem cells at 0 hr, 24hr, 36hr, etc). The user can click on any of the coloured regions or the number of genes within the legend box to view the list of Gene IDs and their annotations. Thereafter, the list can be saved as a data set for future analysis.