Search results for " ontology"
showing 10 items of 175 documents
A multivariate statistical test for differential expression analysis
2022
AbstractStatistical tests of differential expression usually suffer from two problems. Firstly, their statistical power is often limited when applied to small and skewed data sets. Secondly, gene expression data are usually discretized by applying arbitrary criteria to limit the number of false positives. In this work, a new statistical test obtained from a convolution of multivariate hypergeometric distributions, the Hy-test, is proposed to address these issues. Hy-test has been carried out on transcriptomic data from breast and kidney cancer tissues, and it has been compared with other differential expression analysis methods. Hy-test allows implicit discretization of the expression profi…
MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data
2015
Background Identification of marker genes associated with a specific tissue/cell type is a fundamental challenge in genetic and cell research. Marker genes are of great importance for determining cell identity, and for understanding tissue specific gene function and the molecular mechanisms underlying complex diseases. Results We have developed a new bioinformatics tool called MGFM (Marker Gene Finder in Microarray data) to predict marker genes from microarray gene expression data. Marker genes are identified through the grouping of samples of the same type with similar marker gene expression levels. We verified our approach using two microarray data sets from the NCBI’s Gene Expression Omn…
Missense variants in TAF1 and developmental phenotypes: Challenges of determining pathogenicity
2019
We recently described a new neurodevelopmental syndrome (TAF1/MRXS33 intellectual disability syndrome) (MIM# 300966) caused by pathogenic variants involving the X-linked gene TAF1, which participates in RNA polymerase II transcription. The initial study reported eleven families, and the syndrome was defined as presenting early in life with hypotonia, facial dysmorphia, and developmental delay that evolved into intellectual disability (ID) and/or autism spectrum disorder (ASD). We have now identified an additional 27 families through a genotype-first approach. Familial segregation analysis, clinical phenotyping, and bioinformatics were capitalized on to assess potential variant pathogenicity…
Functional annotation of genes overlapping copy number variants in autistic patients: focus on axon pathfinding.
2010
We have used Gene Ontology (GO) and pathway analyses to uncover the common functions associated to the genes overlapping Copy Number Variants (CNVs) in autistic patients. Our source of data were four published studies [1- 4]. We first applied a two-step enrichment strategy for autism-specific genes. We fished out from the four mentioned studies a list of 2928 genes overall overlapping 328 CNVs in patients and we first selected a sub-group of 2044 genes after excluding those ones that are also involved in CNVs reported in the Database of Genomic Variants (enrichment step 1). We then selected from the step 1-enriched list a sub-group of 514 genes each of which was found to be deleted or dupli…
The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae
2021
This article belongs to the Section Molecular Informatics.
Use of Geospatial Analyses for Semantic Reasoning
2010
International audience; This work focuses on the integration of the spatial analyses for semantic reasoning in order to compute new axioms of an existing OWL ontology. To make it concrete, we have defined Spatial Built-ins, an extension of existing Built-ins of the SWRL rule language. It permits to run deductive rules with the help of a translation rule engine. Thus, the Spatial SWRL rules are translated to standard SWRL rules. Once the spatial functions of the Spatial SWRL rules are computed with the help of a spatial database system, the resulting translated rules are computed with a reasoning engine such as Racer, Jess or Pellet.
Einübung in das Denken. Gérard Granels ‚Introduction‘ zu seiner Übersetzung von Martin Heideggers Was heißt Denken?
2018
Im Beitrag wird Gérard Granels "introduction“ zu seiner "traduction" von Heideggers "Was heißt Denken?" vorgestellt, die Ende der Fünfzigerjahre in Zusammenarbeit mit dem deutschen Aloys Becker entstand und 1959 erstmalig bei den Presses Universitaires de France erschien. Dieser sprachlich und gedanklich bemerkenswert dichte Übersetzungskommentar Granels ist im Hinblick auf die Frage nach dem Verhältnis von Theorie und Praxis des Übersetzens, die als Frage nach der Möglichkeit einer Überwindung gestellt wird, umso aufschlussreicher, als bereits die heideggersche Vorlage wesentlich um den Zusammenhang von Denken und Übersetzen, Sprachmaterialität und Sinnschöpfung kreist.
Hermeneutics and Phenomenology Problems When Applying Hermeneutic Phenomenological Method in Educational Qualitative Research
2020
Hermeneutic phenomenology is a research method used in qualitative research in the fields of education and other human sciences, for example nursing science. It is a widely used method example in Scandinavia, and Van Manen is well known for his hermeneutic phenomenological method. In many studies the hermeneutic phenomenological method is inarticulate or ambiguous. Researchers generally lack a common understanding of what this method actually is. One reason for that is that the expression “hermeneutic phenomenological method” is contradiction in terms. Hermeneutics and phenomenology have their own distinct history. Hermeneutics and phenomenology as philosophical disciplines have their own d…
Discovering learning paths on a domain ontology using natural language interaction
2005
The present work investigates the problem of determining a learning path inside a suitable domain ontology. The proposed approach enables the user of a web learning application to interact with the system using natural language in order to browse the ontology itself. The course related knowledge is arranged as a three level hierarchy: content level, symbolic level, and conceptual level bridging the previous ones. The implementation of the ontological, the interaction, and the presentation component inside the TutorJ system is explained, and the first results are presented.
On Using Conceptual Modeling for Ontologies
2004
Are database concepts and techniques suitable for ontology design and management? The question has been on the floor for some time already. It gets a new emphasis today, thanks to the focus on ontologies and ontology services due to the spread of web services as a new paradigm for information management. This paper analyzes some of the arguments that are relevant to the debate, in particular the question whether conceptual data models would adequately support the design and use of ontologies. It concludes suggesting a hybrid approach, combining databases and logic-based services.