Table 3.
General omics and Kidney-specific databases.
| Tool | Data types | Purpose |
|---|---|---|
| Genomics | ||
| GeneCards (http://www.genecards.org/) | Contains >152 000 GeneCards genes; Gene-centric data from approximately 150 network sources; Detailed information on all annotated and predicted human genes | Search for human genetic information; The first key to the study of gene function |
| Online Mendelian Inheritance in Man (http://www.omim.org/) | >15 000 genes; Contains a central database of information and literature on human genetic diseases and genetic loci | Looks for the latest clinical testing standards and trends;Provides detailed information about this class of annotations from gene sequences, maps, literature and other databases |
| NephQTL (http://www.nephqtl.org)* | Compartment-specific (glomeruli and tubulointerstitium) gene expression profiles from biopsy samples of 187 participants in the NEPTUNE cohort; Genotype frequency of SNPs in the NEPTUNE cohort | Compartment-specific (glomerular and tubule) eQTL discovery |
| Human Kidney eQTL Atlas (http://www.susztaklab.com/eqtl)* | Compartment-specific (glomeruli and tubulointerstitium) gene expression profiles from biopsy samples of 151 participants linked to SNP data | Compartment-specific (glomerular and tubule), as well as whole kidney eQTL discovery |
| Transcriptomics | ||
| Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/gds) | 3848 data sets based on arrays and sequences; Storage of chips, second-generation sequencing and other high-throughput sequencing data | Gene expression data repository, data analysis and visualization |
| ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) | 60,054 high-throughput experiments; Storage of chips and high-throughput sequencing data | Arrayexpress database for EBI, similar to GEO database; Archives of Functional Genomics |
| Expression Atlas (https://www.ebi.ac.uk/gxa/) | 1572 data sets; Provides information on gene expression patterns under different biological conditions | More focus on baseline trials |
| miRBase (http://www.mirbase.org) | 28 645 miRNA entries from 223 species; Details of all published and annotated miRNAs | Databases used to study miRNA |
| Nephroseq (https://www.nephroseq.org/)* | 26 data sets (1989 samples); Transcriptome analysis of biopsy samples from patients with renal disease; Clinical metadata from patients | Identifying disease-related signatures; Correlation of gene expression with clinical features |
| Renal Gene Expression Database(RGED) (http://rged.wall-eva.net/)* | 88 research papers analysed; Contains comprehensive gene expression data sets from kidney disease studies | Contains comprehensive gene expression data sets from kidney disease studies; Provides a user-friendly utility for the nephropathy research community |
| Rebuilding a Kidney Consortium (http://www.rebuildingakidney.org)* | scRNA-seq visualizations from kidney biopsy samples, model systems and organoids; Shared resources with GUDMAP Lab protocols; Antibody validation; Cataloguing of iPSC lines | Coordinate studies and data relevant to nephron regeneration; Primary data access |
| Nephrocell (http://nephrocell.miktmc.org/)* | scRNA-seq data from kidney biopsy samples and organoids | Cell-selective gene marker identification |
| Proteomics | ||
| PRoteomics IDEntifications (PRIDE) (https://www.ebi.ac.uk/pride/archive/) | Store 3342 items for protein/peptide identification, post-translational modifications, and supporting spectral evidence; One of the most prominent data repositories for proteomic data based on mass spectrometry (MS); Allows viewing of 2d gels and query scores | To enable the proteomics community to share publicly or in private partnerships the vast amounts of data generated by proteomics laboratories around the world. |
| Human Protein Atlas (http://www.proteinatlas.org/) | 213 tissue and cell line samples; Proteomic analysis based on 24,028 antibodies against 16,975 unique proteins | To understand the expression of human protein in tissues, cell localization and pathological expression. |
| Human Kidney and Urine Proteome Project (HKUPP) (http://www.hkupp.org/)* | Look for proteins in renal structures (glomerulus, human medulla) and urine; Allows viewing of 2d gels and query scores | To promote proteomics research in the field of nephrology to better understand kidney function and the pathogenesis of kidney disease, and to define new biomarkers and therapeutic targets. |
| Urinary Protein Biomarker Database (http://122.70.220.102/biomarker)* | > 400 reports on humans and animals; 819 human biomarkers and 33 animal biomarkers were collected from the published literature | To obtain urinary protein specific biomarker candidates |
| Metabolomics | ||
| Human Metabolome Database(HMDB) (http://www.hmdb.ca/) | Contains experimental MS/MS data for more than 5,700 compounds, experimental 1 H and 13 C NMR data (and allocation) for more than 1,300 compounds, and GC/MS spectral and retention index data for more than 780 compounds; | Obtain detailed information about metabolites and their associations with pathways, proteins, and reactions |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) | One of the most complete and widely used databases containing metabolic pathways (495 reference pathways) from a variety of organisms (>4,700) | Understand a repository of advanced features and utilities for biological systems; |
| (https://www.kegg.jp) | >17,000 compounds, 10,000 drugs and nearly 11,000 glycan structures | With powerful graphics function, more intuitive and comprehensive understanding of metabolic pathways |
| Metabolite Link (Metlin) (https://metlin.scripps.edu) | >240,000 metabolites and 72,000 high resolution MS/MS spectrograms; A repository of mass spectrometry metabolite data | Emphasis should be placed on the identification of non-targeted Metabolomics metabolites in liquid |
| The Small Molecule Pathway Database(SMPDB) (http://smpdb.ca/) | 910 hand-painted small molecule metabolic pathways, including 468 drug pathways, 232 disease pathways, 105 metabolic pathways and more than 100 other pathways; A database of interactive, visual small molecular pathways | Cleverly detailed hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways, and drug activity pathways |
| Multi-omics | ||
| Multi-Omics Profiling Expression Database (MOPED) (http://moped.proteinspire.org) | Absolute and relative protein expression data from more than 250 large-scale experiments; >500,000 proteomic absolute and relative expression records; >500,000 proteomic absolute and relative expression records; Relative gene expression data | Used to query different types of omics expression data and data visualization; View expression data, pathway mapping, and direct connections between proteins and genes; Provides a background for the exploration of multiple omics expressive data |
| Kidney Systems Biology Project (https://hpcwebapps.cit.nih.gov/ESBL/Database/)* | Transcriptomic, protein, Chip-seq data from model systems and renal epithelial cells | Gene- and protein-centred queries in kidney tissues, cells and segments |
| Kidney and Urinary Pathway Knowledge Base (KUPKB) (http://www.kupkb.org/)* | > 220 experiments; Contains data from renal and urinary high-throughput experiments, with rich links to other biological data, forming a single integrated repository | Collect open omics data related to kidney disease |