A powerful feature of the InterMine framework is the analysis of features lists e.g genes or proteins. Users can store gene lists for example and list of differentially expressed genes from a specific RNASeq experiment then performing GO-term enrichment analysis on such lists.
The list tool searches the database for the list items and attempts to convert each identifier to the selected type. User can create list from Quick List box on the home page or by clicking on the Lists tab from the menu to access the full list upload as seen in Fig. 11.
Creating list example¶
As an example, enter the following identifiers (comma-separated):
ASH1, CAL0000174561, FTR1,CAS1,CR_08980C_A
Leave the Select Type as “Gene” and Organism drop-down as “Any”. Then click Create List. A Summary table is displayed with the results of searching for each of the five identifiers in the list Fig. 12.
Next, click Save a list of 5 Genes. A List Analysis page is presented that contains widgets allowing users to perform analyses on the genes in the list.
The available widgets are:
- Chromosome Distribution.
- Gene Ontology Enrichment.
- Protein Domain Enrichment.
- Domains from Proteins
- Predicted Domains from genes.
- Phenotypes (APO).
- Pathway Enrichment.
- Publication Enrichment.
The selection of widgets provided on the List Analysis page depend on the contents of the list.
Saved lists appear under the View tab on the Lists page. For users who are not logged in, lists are saved temporarily; users must log in to save lists permanently. Saved lists may also be accessed from the MyMine menu item.
Predefined lists of all genes from different species are also available on the Lists page for all users.