OncoLand Case Study - OncoGEO
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OncoGEO case Study: Anti-PD1 resistance
A recent paper examined the differences in gene expression of metastatic melanomas from patients that are resistant or responsive to anti-PD1 therapy. We can use OncoGEO to browse the results from comparisons using this data and find additional studies that may have similar gene set enrichment.
Study Background - anti-PD1 Therapy
Filtering and Identification of samples of interest
Studies incorporated into OncoGEO are curated by Omicsoft scientists using a controlled vocabulary. This allows users to quickly search and filter for studies using sample and project metadata, along with browse the different comparisons precomputed within the Land, using distribution views. Once projects or samples are identified, users can use the metadata to group samples based on factors of interest. For studies including survival data, users can generate survival views based on the groupings within the land.
Browsing project-level comparison data and gene set analysis
Users can browse all project-level information in the search bar at the top of the screen. As in the Analysis tab of Array Studio, the views in Land are completely customizable. Once inference reports within the Land have been identified, users can search for similar gene set enrichment using the Gene Set Analysis view. Here, we find that genes differentially expressed in anti-PD1 resistant vs responding samples overlap with gene sets identified in a MAPKi resistance study.
Browsing multiple comparisons
There are a number of views available to users to browse multiple comparisons to see where there is overlapping gene regulation. Data from Land can easily be exported in table format or directly upload to Ingenuity Pathway Analysis (IPA) for further analysis.