KPMP Atlas Explorer tool released

KPMP Atlas Explorer tool released

September 6, 2021

The Kidney Precision Medicine Project (KPMP) is proud to announce the release of the Atlas Explorer Tool (https://atlas.kpmp.org/explorer/), This tool allows you to search by marker gene, cell type, or data type to view summary data visualizations across the various KPMP 'omics' technologies.

 

“Biomedical science is opening up incredible opportunities to learn about the molecular disease process for patients. For kidney disease we have the unique opportunity to capture them in kidney biopsies. In KPMP we have now a pipeline in place to generate this information at an unprecedented depth. The art is to present this data in such a way that it connects easily with the different users of the Atlas, representing a variety of backgrounds and interests. We have a great team to help to make our data accessible and make a difference.” noted Dr. Matthias Kretzler, Principal Investigator for the KPMP Data Visualization Center (DVC).

For each KPMP participant, kidney tissue is obtained for molecular phenotyping and clinical diagnosis. In addition to the kidney biopsy tissue, the study collects baseline(time of biopsy) and longitudinal biospecimens (including urine, plasma, serum, DNA, and stool) and demographic, clinical, and laboratory data. Kidney biopsy tissue is processed to allow for multiple -omics technologies to be run on the same participant. Technologies that have been approved to receive participant biopsy tissue include: 3D imaging/cytometry, CODEX, regional proteomics, regional transcriptomics, single-nucleus RNA-seq, single-cell RNA-seq, and spatial metabolomics.

Of the above technologies, three datatypes have been incorporated into the first version of the Atlas Explorer to-date: single-nucleus RNA-seq, single-cell RNA-seq, and regional transcriptomics.

Total Participants in Atlas Explorer v1.0 for Each Data Type

 OMICS TYPE  HEALTHY REFERENCE  CKD AKI
 Single-nucleus RNA-seq (snRNA-seq) 3 10 6
 Single-cell RNA-seq (scRNA-seq) 15  12 
 Regional transcriptomics (LMD RNA-seq) 22 

As noted above, the Atlas Explorer Tool allows users to search by marker gene, cell type, or datatype and see the associated data. Searching for a gene presents the user with various visualizations and data tables displaying how the gene is expressed in the selected data type. Users can also begin by searching for a cell type instead of a gene. After searching for a cell type or selecting one from the renal corpuscle or nephron schemata, a user can see all the differentially expressed genes currently mapped to that cell type (or its associated structure) across the various available technologies. More information about navigating the Explorer tool can be found at https://www.kpmp.org/help-docs/software and via the video below.

“We are excited to bring this first iteration of the Atlas Explorer to the kidney research community, as it brings together transcriptomics data from multiple resolutions to aid in the identification of kidney disease subgroups and critical kidney cells, pathways, and targets for novel therapies for AKI and CKD. We look forward to expanding the Atlas Explorer with additional datasets and features in the coming months,” said Becky Steck, Operations Director for the DVC.

The KPMP Atlas Explorer was developed by the KPMP Central Hub Data Visualization Center at the University of Michigan. The underlying code is freely accessible from our KPMP GitHub page.