Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization

Abstract

The clinical sampling of urine is noninvasive and unrestricted, whereby huge volumes can be easily obtained. This makes urine a valuable resource for the diagnoses of diseases. Urinary and renal proteomics have resulted in considerable progress in kidney-based disease diagnosis through biomarker discovery and treatment. This review summarizes the bioinformatics tools available for this area of proteomics and the milestones reached using these tools in clinical research. The scant research publications and the even more limited bioinformatic tool options available for urinary and renal proteomics are highlighted in this review. The need for more attention and input from bioinformaticians is highlighted, so that progressive achievements and releases can be made. With just a handful of existing tools for renal and urinary proteomic research available, this review identifies a gap worth targeting by protein chemists and bioinformaticians. The probable causes for the lack of enthusiasm in this area are also speculated upon in this review. This is the first review that consolidates the bioinformatics applications specifically for renal and urinary proteomics.

Keywords: bioinformatics; databases; omics; renal; tools; urinary proteomics.

Figure 1

Statistics on research publications related to urinary and renal proteomics, obtained from a Pubmed database search.

Figure 2

Comparative graph on research published in the area of bioinformatics/biocomputation and proteomics versus bioinformatics/biocomputation and renal and urinary proteomics.

Figure 3

A schematic of the work flow of urinary proteomics research, showing points of interaction where bioinformatics tools are useful. The first step involves the collection of samples from healthy and diseased populations, followed by protein extraction and digestion, prior to analysis using analytical tools. The output data is what is subjected to bioinformatics analysis. UMDB—Urine Metabolome database; HPRD—Human Protein Reference Database; KUPKB—Kidney and Urinary Pathway Knowledge Base; UPdb—Human Urinary Proteomic Fingerprint Database; GEO—Gene Expression Omnibus; MSOmics—The metabolomics service experts.