VaProS: a database-integration approach for protein/genome information retrieval

Abstract

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

Specific Features of Fibrotic Lung Fibroblasts Highly Sensitive to Fibrotic Processes Mediated via TGF-β–ERK5 Interaction

“…A pathway enrichment analysis was performed for upand downregulated differentially expressed genes (DEGs; for statistics, see next subsection) in fibrotic lung fibroblasts using the Reactome database [21] (version V62). To determine whether DEGs belonged to an enriched pathway that could be linked to TGF-β1 or ERK5, protein interaction networks were constructed with VaProS [22] using the "Via Path Search" function. We used Cytoscape 3.6.1 [23] to visualize these networks.…”

A case of a heterozygous ABCC6 mutation showing recurrent ischemic strokes and intracranial hemorrhages

“…Consequently, we assessed the functional impact of this mutation by S-VAR, which evaluates the impact of a mutation using multiple software. 9,10 According to the evaluation by S-VAR, the impact of this mutation is probably damaging (PolyPhen2) or deleterious (SIFT, PROVEN, and PANTHER). 9,10 Thus, we suspected that this mutation may have had some effect on the patient's clinical features.…”

Biophysics at Waseda University

“…Many students have graduated from the lab and have academic positions in universities now. The topic of their study has since diverged from the original folding problem to protein evolution, protein design, protein dynamics, and protein function prediction and integrated database building for genome and proteome (Gojobori et al 2016). Although the topic has diverged and the number of application-oriented research has increased, the spirit of biophysics research in Waseda University has remained the same, which is to find physical principles in biological systems.…”