Comment on 'Hayai-Annotation plants: an ultra-fast and comprehensive functional gene annotation system in plants'. The importance of taking the GO graph structure into account.
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ABSTRACT:
SUBMITTER: Van Bel M
PROVIDER: S-EPMC8016466 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:SummaryHayai-Annotation Plants is a browser-based interface for an ultra-fast and accurate functional gene annotation system for plant species using R. The pipeline combines the sequence-similarity searches, using USEARCH against UniProtKB (taxonomy Embryophyta), with a functional annotation step. Hayai-Annotation Plants provides five layers of annotation: i) protein name; ii) gene ontology terms consisting of its three main domains (Biological Process, Molecular Function and Cellular Component); iii) enzyme commission number; iv) protein existence level; and v) evidence type. It implements a new algorithm that gives priority to protein existence level to propagate GO and EC information and annotated Arabidopsis thaliana representative peptide sequences (Araport11) within 5 min at the PC level.Availability and implementationThe software is implemented in R and runs on Macintosh and Linux systems. It is freely available at https://github.com/kdri-genomics/Hayai-Annotation-Plants under the GPLv3 license.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC6821316 | biostudies-literature
Project description:As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.
| S-EPMC4714749 | biostudies-literature
Project description:Transcriptome of plants exposed to 0, 20 and 60 sec light stress was analyzed using Illumina HiSeq2000. We found that mRNA accumulation of more than 700 transcripts in plants occurs as early as 20-60 sec following light stress application
2016-12-06 | GSE60865 | GEO
Project description:Feedback delays are a major challenge for any controlled process, and yet we are able to easily control limb movements with speed and grace. A popular hypothesis suggests that the brain largely mitigates the impact of feedback delays (∼50 ms) by regulating the limb intrinsic visco-elastic properties (or impedance) with muscle co-contraction, which generates forces proportional to changes in joint angle and velocity with zero delay. Although attractive, this hypothesis is often based on estimates of limb impedance that include neural feedback, and therefore describe the entire motor system. In addition, this approach does not systematically take into account that muscles exhibit high intrinsic impedance only for small perturbations (short-range impedance). As a consequence, it remains unclear how the nervous system handles large perturbations, as well as disturbances encountered during movement when short-range impedance cannot contribute. We address this issue by comparing feedback responses to load pulses applied to the elbow of human subjects with theoretical simulations. After validating the model parameters, we show that the ability of humans to generate fast and accurate corrective movements is compatible with a control strategy based on state estimation. We also highlight the merits of delay-uncompensated robust control, which can mitigate the impact of internal model errors, but at the cost of slowing feedback corrections. We speculate that the puzzling observation of presynaptic inhibition of peripheral afferents in the spinal cord at movement onset helps to counter the destabilizing transition from high muscle impedance during posture to low muscle impedance during movement.
| S-EPMC4191878 | biostudies-literature
Project description: Not available
| S-EPMC4214588 | biostudies-literature
Project description:Transcranial alternating current stimulation (tACS) has found widespread use as a basic tool in the exploration of the role of brain oscillations. Many studies have shown that frequency-specific tACS is able to not only alter cognitive processes during stimulation, but also cause specific physiological aftereffects visible in the electroencephalogram (EEG). The relationship between the emergence of these aftereffects and the necessary duration of stimulation is inconclusive. Our goal in this study was to narrow down the crucial length of tACS-blocks, by which aftereffects can be elicited. We stimulated participants with α-tACS in four blocks of 1-, 3-, 5-, and 10-min length, once in increasing and once in decreasing order. After each block, we measured the resting EEG for 10 min during a visual vigilance task. We could not find lasting enhancement of α-power following any stimulation block, when comparing the stimulated groups to the sham group. These findings offer no information regarding the crucial stimulation duration. In addition, this conflicts with previous findings, showing a power increase following 10 min of tACS in the alpha range. We performed additional explorative analyses, based on known confounds of (1) mismatches between stimulation frequency and individual alpha frequency and (2) abnormalities in baseline α-activity. The results of an ANCOVA suggested that both factor explain variance, but could not resolve how exactly both factors interfere with the stimulation effect. Employing a linear mixed model, we found a significant effect of stimulation following 10 min of α-tACS in the increasing sequence and a significant effect of the mismatch between stimulated frequency and individual alpha frequency. The implications of these findings for future research are discussed.
| S-EPMC6019480 | biostudies-literature
Project description:Day-to-day variability in microarray experiments is a recognized source of variation that can impede the analysis of large microarray studies where samples are processed on different days. In this study, we have applied an algorithm, called D2Dsum, which is based on a log-linear fixed effect model to cope with this kind of issues on a data set of 45 microarrays. Keywords: time course
2007-12-12 | GSE9826 | GEO
Project description:Currently, food waste is estimated at more than one-third of all food produced, and the primary responsibility for this phenomenon is attributed to households. Therefore, it seems reasonable to take action to limit food waste and to raise awareness about this link in the chain. To develop and implement educational programs addressed at consumers it is necessary to understand the factors determining food waste in households. Segmentation is a tool that can help effectively reach consumers who are to the greatest extent wasting food which identifies homogeneous clusters of consumers. The aim of this study was to perform segmentation to identify consumer groups with similar behaviors in relation to food, with particular emphasis on food wastage. We carried out segmentation on a representative sample of Polish people over 18 years of age and to identified three clusters of consumers. The three consumer segments diagnosed differed in sociodemographic terms, i.e., number of adults, number of children, subjective assessment of the financial situation, and percentage of spending on food. The segment exhibiting a high frequency of discarding food due to too large package size included single and double households.
| S-EPMC7230927 | biostudies-literature
Project description:Simulations are used to generate plausible realisations of soil and climatic variables for input into an enterprise land suitability assessment (LSA). Subsequently we present a case study demonstrating a LSA (for hazelnuts) which takes into account the quantified uncertainties of the biophysical model input variables. This study is carried out in the Meander Valley Irrigation District, Tasmania, Australia. It is found that when comparing to a LSA that assumes inputs to be error free, there is a significant difference in the assessment of suitability. Using an approach that assumes inputs to be error free, 56% of the study area was predicted to be suitable for hazelnuts. Using the simulation approach it is revealed that there is considerable uncertainty about the 'error free' assessment, where a prediction of 'unsuitable' was made 66% of the time (on average) at each grid cell of the study area. The cause of this difference is that digital soil mapping of both soil pH and conductivity have a high quantified uncertainty in this study area. Despite differences between the comparative methods, taking account of the prediction uncertainties provide a realistic appraisal of enterprise suitability. It is advantageous also because suitability assessments are provided as continuous variables as opposed to discrete classifications. We would recommend for other studies that consider similar FAO (Food and Agriculture Organisation of the United Nations) land evaluation framework type suitability assessments, that parameter membership functions (as opposed to discrete threshold cutoffs) together with the simulation approach are used in concert.
| S-EPMC4627905 | biostudies-literature
Project description: Not available
| S-EPMC518904 | biostudies-literature