ABOUT GeneSetCart
To facilitate data integration, discovery, and hypothesis generation across diverse Common Fund programs' datasets, highly processed data can be converted into gene-, metabolite- and drug-set libraries. Such abstracted versions of the data facilitate data integration and discovery. GeneSetCart is an interactive web-based application that enables users to fetch gene sets from various Common Fund programs data sources, augment these sets with gene-gene co-expression correlations or protein-protein interactions, perform set operations such as union, consensus, and intersection on multiple sets, visualize and analyze these gene sets in a single session. GeneSetCart provides access to CFDE generated gene sets through a term query interface that returns gene sets related to all biomedical terms sourced from most CFDE DCCs. GeneSetCart also supports the upload of single and multiple user-generated gene sets. Users of GeneSetCart can also obtain gene sets by searching PubMed for genes co-mentioned with any term in publications. Visualizations of gene sets from the various sources can be generated in the form of publication-ready Venn diagrams, heatmaps, UMAP, SuperVenn diagrams, and UpSet plots that summarize the overlap and similarity between sets. Users can also perform functional enrichment analysis of their assembled gene sets through external links to gene set analysis tools such as Enrichr, CFDE-GSE, Rummagene, RummaGEO, Kinase Enrichment Analysis (KEA3), and Chip-X Enrichment Analysis (ChEA3). All gene sets added or created in a session can be saved to a user account for re-analysis and reproducibility and also shared to others. GeneSetCart also has a GMT Crossing feature where users can cross CF sourced gene set libraries to can find gene sets with a significant number of overlapping genes originated from different CF programs. The crossed pairs are displayed in an interactive table on the CFDE GMT Crossing page . Users can also view a GPT-4-generated hypothesis proposing a possible reason for the high overlap between these sets. Overall, GeneSetCart is a useful resource to facilitate hypothesis generation across CF datasets and programs.
Gene set libraries are regularly updated from the GMT files submitted by CFDE programs on the CFDE Data Portal .
GeneSetCart is actively being developed by the Ma'ayan Lab .
TERMS OF SERVICE
Use
GeneSetCart is protected GNU GENERAL PUBLIC LICENSE Version 3.
Disclaimer
This site is not intended for treating or diagnosing human subjects.
The tools, services, and any associated materials or documents provided by this site are made available as-is without any warranty of any kind, either express, implied, or statutory. This includes, but is not limited to, implied warranties of merchantability, fitness for a particular purpose, or non-infringement.
We do not guarantee that the tools or services will be error-free, secure, or free from interruptions. We also cannot make assurances that your use of the tools or documents will not infringe upon the intellectual property or proprietary rights of third parties.
Data Security and Privacy
While we will never intentionally share any gene sets or data that you store on the site, we cannot guarantee their security. Users are encouraged to avoid uploading sensitive or proprietary information.
Additionally, if any data is sent to third-party services, including OpenAI, we cannot control how that data is shared, stored, or used by those services. By using this site, you acknowledge and accept this risk.
Liability
In no event will we or any affiliated entities, including developers, researchers, or institutions, be liable for any damages, including but not limited to direct, indirect, special, or consequential damages, arising out of, resulting from, or in any way connected with the use of this site or associated documents.
Acknowledgment
By using this site, you acknowledge that you have read, understood, and agree to these terms and conditions.