Identification of domains from protein sequences

Center Variation and the Effect of Center and Provider Characteristics on Clinical Outcomes in Kidney Transplantation: A Systematic Review of the Evidence

Background

Kidney transplantation is the best treatment option for patients with end-stage renal disease. While patient-level factors affecting survival are established, the presence of variation in the management of transplant recipients remains unknown.

Objective

The objective of this study was to examine center variation in kidney transplantation and identify center and provider characteristics that may be associated with clinical outcomes.

Design

This is a systematic review.

Data sources

Ovid Medline, Embase, and Cochrane library from inception to June 2016 were used.

Study eligibility

Any study examining the association between center or provider characteristics and graft or patient survival, quality of life, or functional status were included.

Results

We identified 6327 records and 24 studies met eligibility. Most studies used data registries. Characteristics evaluated include center volume (n = 17), provider volume (n = 2), provider experience (n = 1), center type (n = 2), and location of follow-up (n = 1). Outcomes assessed included graft survival (n = 24) and patient survival (n = 9). Significant center variation was described in 12 of 15 and 5 of 7 studies for graft and patient survival. There was a significant and positive association between center volume and graft and patient survival in 8 and 2 studies, respectively. Provider experience and volume were significantly associated with less allograft loss and provider volume with lower risk of death. There was no association between graft survival and location of follow-up or center type.

Limitations

There was substantial heterogeneity in the variables assessed and methodology used to analyze associations.

Conclusion

This systematic review found center variation in kidney transplantation. Future studies in the current era are necessary to better evaluate this important topic.

THoR: a tool for domain discovery and curation of multiple alignments

We describe a tool, THoR, that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family. The entire process is designed for use via a web-browser, with simple links and cross-references to relevant information, to assist the assessment of biological significance. THoR has been benchmarked for accuracy using the SMART and pufferfish genome databases.

Predicting protein cellular localization using a domain projection method

We investigate the co-occurrence of domain families in eukaryotic proteins to predict protein cellular localization. Approximately half (300) of SMART domains form a "small-world network", linked by no more than seven degrees of separation. Projection of the domains onto two-dimensional space reveals three clusters that correspond to cellular compartments containing secreted, cytoplasmic, and nuclear proteins. The projection method takes into account the existence of "bridging" domains, that is, instances where two domains might not occur with each other but frequently co-occur with a third domain; in such circumstances the domains are neighbors in the projection. While the majority of domains are specific to a compartment ("locale"), and hence may be used to localize any protein that contains such a domain, a small subset of domains either are present in multiple locales or occur in transmembrane proteins. Comparison with previously annotated proteins shows that SMART domain data used with this approach can predict, with 92% accuracy, the localizations of 23% of eukaryotic proteins. The coverage and accuracy will increase with improvements in domain database coverage. This method is complementary to approaches that use amino-acid composition or identify sorting sequences; these methods may be combined to further enhance prediction accuracy.