HumanBase User Guide¶
HumanBase is a “one stop shop” for biological and biomedical researchers interested in data-driven predictions of gene expression, function, regulation, and interactions in human, particularly in the context of specific cell types/tissues, development, and human disease.
Data-driven integrative analyses are especially powerful because they reach beyond “known biological knowledge” represented in the biological literature to identify novel associations that are not biased toward well-studied areas of biomedical research. Thus, carefully designed algorithms can drive the development of experimentally testable hypotheses, enabling deeper understanding of basic biology at the molecular level, pathophysiology, and paving the way to therapy and drug development.
Example use case¶
A researcher who studies the role of the immune system and inflammation in chronic kidney disease wants to identify candidate genes for these disorders. Unfortunately, as with most specific disease contexts outside of cancer, few datasets are available for these diseases, none are focused on the role of inflammation or the immune system, and no dataset is specific to her cell-lineage of interest. Even identifying which genes are expressed in the cell type relevant to glomerular disease (podocytes) is currently impossible as this cell lineage cannot be isolated for high-throughput experiments in human.
Using HumanBase, she will be able to examine data-driven predictions of genes expressed in the podocyte cells and analyze predicted functional and mechanistic networks specific to the kidney glomerulus. She could also provide the system with a list of relevant GWAS or family-based study results and the system will reprioritize these results based on the relevant functional maps. She will be able to iteratively refine this analysis by limiting the data used in the integration only to kidney datasets or by integrating her own data in the analysis.
All data in HumanBase are freely available under a CC-BY 4.0 license. Please give appropriate credit, provide a link to the license, and indicate if changes were made.
Who are we?¶
HumanBase is actively developed by the Genomics group at the Flatiron Institute .
- Getting Started
- Functional Networks
- Tissue-specific Networks
- Functional module detection
- NetWAS - Network-wide Association Study
- DeepSEA (Beluga)
- SEEK - Search-Based Exploration of Expression Compendium