Table 2.
Kidney-specific databases
| Name | Description | Main features |
|---|---|---|
| Transcriptomics | ||
| Nephroseq (https://www.nephroseq.org/) | Gene expression in renal disease; integration with clinical data | 26 datasets (1989 samples) |
| Analysis and visualization tools (differential expression, co-expression, outlier, etc.) | ||
| Upload and export tools | ||
| Renal Gene Expression Database (http://rged.wall-eva.net/) | Gene expression in renal disease | 88 research papers analysed |
| Easy-to-use interface | ||
| Proteomics | ||
| Human Kidney and Urine Proteome Project (HKUPP) (http://www.hkupp.org/) | Protein expression in normal urine and normal or diseased kidney | Search for proteins in kidney structures (glomerulus, human medulla) and urine |
| Enables viewing two-dimensional gels and query fractions | ||
| Urinary Protein Biomarker Database (http://122.70.220.102/biomarker) | Candidate protein biomarkers in urine | >400 reports on human and animals |
| 819 human biomarkers, 33 animal biomarkers | ||
| Peptidomics | ||
| Urinary Peptidomics and Peak-maps (http://www.padb.org/updb) | Urinary peptides modified in disease | Search by detection methodology and disease |
| Multi-omics | ||
| Kidney and Urinary Pathway Knowledge Base (KUPKB) (http://www.kupkb.org/) | Collection of publically available omics data related to renal disease | >220 experiments |
| Easy and fast interface | ||
| Pathway visualization with KUPKB Network Visualizer | ||
| Chronic Kidney Disease database (CKDdb) (http://www.padb.org/ckddb) | Collection of publically available omics data related to chronic kidney disease | 366 datasets |
| Search by study, sample, tissue, disease and molecule type | ||