The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equivalent variants, namely ‘matching variants’ (MatchVars) between humans and other organisms. Therefore, we developed an integrated search engine called ConVarT (http://www.convart.org/) for matching variants between humans, mice, and Caenorhabditis elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic MatchVars from mice and C. elegans can give clues about the functional consequence of human genetic variants. Our analysis shows that many phenotypic variants in different genes from mice and C. elegans, so far, have no counterparts in humans, and thus, can be useful resources when evaluating a relationship between a new human mutation and a disease.
Age-associated deterioration of cellular physiology leads to pathological conditions. The ability to detect premature aging could provide a window for preventive therapies against age-related diseases. However, the techniques for determining cellular age are limited, as they rely on a limited set of histological markers and lack predictive power. Here, we implement GERAS (GEnetic Reference for Age of Single-cell), a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displays greater than 90% accuracy in classifying the chronological stage of zebrafish and human pancreatic cells. The framework demonstrates robustness against biological and technical noise, as evaluated by its performance on independent samplings of single-cells. Additionally, GERAS determines the impact of differences in calorie intake and BMI on the aging of zebrafish and human pancreatic cells, respectively. We further harness the classification ability of GERAS to identify molecular factors that are potentially associated with the aging of beta-cells. We show that one of these factors, junba, is necessary to maintain the proliferative state of juvenile beta-cells. Our results showcase the applicability of a machine learning framework to classify the chronological stage of heterogeneous cell populations, while enabling detection of candidate genes associated with aging.
The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equivalent variants, namely “orthologous variants,” between humans and other organisms. Therefore, we developed an integrated search engine called ConVarT (http://www.convart.org/) for orthologous variants between humans, mice, and C. elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic OrthoVars from mice and C. elegans can give clues about the functional consequence of human genetic variants. Our analysis shows that many phenotypic variants in different genes from mice and C. elegans, so far, have no counterparts in humans, and thus, can be useful resources when evaluating a relationship between a new human mutation and a disease.Graphical Abstract
Motivation Predicting secondary structure and solvent accessibility of proteins are among the essential steps that preclude more elaborate 3D structure prediction tasks. Incorporating class label information contained in templates with known structures has the potential to improve the accuracy of prediction methods. Building a structural profile matrix is one such technique that provides a distribution for class labels at each amino acid position of the target. Results In this paper, a new structural profiling technique is proposed that is based on deriving PFAM families and is combined with an existing approach. Cross-validation experiments on two benchmark datasets and at various similarity intervals demonstrate that the proposed profiling strategy performs significantly better than Homolpro, a state-of-the-art method for incorporating template information, as assessed by statistical hypothesis tests. Availability and implementation The DSPRED method can be accessed by visiting the PSP server at http://psp.agu.edu.tr. Source code and binaries are freely available at https://github.com/yusufzaferaydin/dspred. Supplementary information Supplementary data are available at Bioinformatics online.
Sequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA, or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic variations, modifications such as post-translational modifications, and annotations (i.e. protein domains). Here, we develop the MSABrowser tool that makes it easy to co-visualize genetic variations, modifications, and annotations on the respective positions of amino acids or nucleotides in pairwise or multiple sequence alignments. MSABrowser is developed entirely in JavaScript and works on any modern web browser at any platform including Linux, Mac OS X, and Windows systems without any installation. MSABrowser is also freely available for the benefit of the scientific community.
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