Focus on inflammatory bowel disease pathways: data resources and analyses on the platform
A few weeks ago we wrote about the extensive updates to the CURIE Knowledge Graph (reaching 1 billion data-driven and literature-mined relations) and a new Data Resources framework in DataHub for semantic integration and indexing of thousands of datasets.
To demonstrate the power and utility of the new datasets and tools on the platform, this week we will focus on one example utilizing data resources associated with ulcerative colitis (UC). The CURIE Entity Page for ulcerative colitis currently includes 30+ UC datasets fully analyzed on the platform. One of these resources comprises of recent data from the Human Microbiome Project (HMP2).
From the Resource view of the HMP2 study, we can access the Pathway Expression App analysis of the associated data which reveals key UC-associated pathways and finds FCGR3A among the top upregulated genes in the HMP2 ulcerative colitis host transcriptome study.
The ulcerative colitis Entity Page shows that FCGR3A upregulation is not only observed in the HMP2 UC dataset but is also found to be consistently upregulated across 25 other UC studies on the platform.
Molecular network analysis of the 30+ integrated datasets shows that FCGR3B (along with FCGR3A) lies within a group of genes regulated by FOXP3. Apart from FOXP3, a few of the other key master regulators uncovered via unbiased network analysis include STAT3 and NFKB1.
The data-driven molecular network can be compared to the canonical inflammatory bowel disease pathways (also available on the platform) to investigate how these three regulators affect other known disease genes and genes suggested directly by the integrated data across 30+ studies.
This is just one small example of moving beyond analyzing one dataset at a time to leveraging thousands of semantically-linked datasets available on the platform to test hypotheses or gain new data-driven insights into a disease of interest. We will provide new case studies with other recent data sources in future posts in the weeks to come.
Now let’s turn data into cures.
We hope you found this update useful. As always, we’d love to hear from you. Write to us at firstname.lastname@example.org. Let us know how we can help and let’s turn data into cures!
— The Data4Cure Team.