Search results for "profiling"
showing 10 items of 881 documents
Sparse kernel methods for high-dimensional survival data
2008
Abstract Sparse kernel methods like support vector machines (SVM) have been applied with great success to classification and (standard) regression settings. Existing support vector classification and regression techniques however are not suitable for partly censored survival data, which are typically analysed using Cox's proportional hazards model. As the partial likelihood of the proportional hazards model only depends on the covariates through inner products, it can be ‘kernelized’. The kernelized proportional hazards model however yields a solution that is dense, i.e. the solution depends on all observations. One of the key features of an SVM is that it yields a sparse solution, dependin…
Tests for Differentiation in Gene Expression Using a Data-Driven Order or Weights for Hypotheses
2005
In the analysis of gene expression by microarrays there are usually few subjects, but high-dimensional data. By means of techniques, such as the theory of spherical tests or with suitable permutation tests, it is possible to sort the endpoints or to give weights to them according to specific criteria determined by the data while controlling the multiple type I error rate. The procedures developed so far are based on a sequential analysis of weighted p-values (corresponding to the endpoints), including the most extreme situation of weighting leading to a complete order of p-values. When the data for the endpoints have approximately equal variances, these procedures show good power properties…
Classification trees for multivariate ordinal response: an application to Student Evaluation Teaching
2016
Data from multiple items on an ordinal scale are commonly collected when qualitative variables, such as feelings, attitudes and many other behavioral and health-related variables are observed. In this paper we introduce a method to derive a distance-based tree for multivariate ordinal response that allows, when subject-specific characteristics are available, to derive common profiles for respondents giving the same/similar multivariate ratings. Special attention will be paid to the performance comparison in terms of AUC, for three different distances used as splitting criteria. Simulated data an a dataset from a Student Evaluation of Teaching survey will be used as illustrative examples. Th…
Iterative Cluster Analysis of Protein Interaction Data
2004
Abstract Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarchical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are consid…
A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data
2015
Abstract Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available appli…
RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing
2012
Abstract Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving. Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression pr…
Structure Learning in Nested Effects Models
2007
Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs of phenotyping studies, e.g., the effects showing in gene expression profiles or as morphological features of the perturbed cell. In this paper we expand the statistical basis of NEMs in four directions. First, we derive a new formula for the likelihood function of a NEM, which generalizes previous results for binary data. Second, we prove model identifiability under mild assumptions. Third, we show that the new formulation of the likelihood allows efficiency in traversing model space. Fourth, we…
Approaches for a Sustainable Use of the Bioactive Potential in Sponges: Analysis of Gene Clusters, Differential Display of mRNA and DNA Chips
2003
In recent years, analyses of the genome organization of marine sponges have begun that have led to the elucidation of selected genes and gene arrangements that exist in gene clusters (e.g. the receptor tyrosine kinase cluster and the allograft inflammatory factor cluster). Most of these studies were performed with the demosponge Suberites domuncula; but Geodia cydonium (Demospongiae), Aphrocallistes vastus (Hexactinellida) and Sycon raphanus (Calcarea) were also investigated. Both S. domuncula and G. cydonium possess a surprisingly large genome of approximately 1.7 pg DNA per haploid set. Taking the high gene density in these sponges into account and considering that predominantly single-co…
Profiling deaf and hard-of-hearing users of subtitles for the deaf and hard-of-hearing in Italy: a questionnaire-based study
2012
The aim of this article is to present the results of a questionnaire-based study carried out as part of the author’s Master’s Degree dissertation about Subtitles for the Deaf and Hard-of-hearing (SDH). In particular, the need to gather specific information regarding audience design will be highlighted in the paper, since this research field has long been neglected in Italy. The questions were aimed at shedding light on the needs, cultural environment and world-view of Italian SDH users, by eliciting personal data as well as subtitlerelated information. Moreover, the 232 respondents were asked to suggest improvements to SDH services in Italy. Although these first results cannot allow definit…
Near-surface defect profiling with slow positrons: Argon-sputtered Al(110).
1985
We report on slow-positron measurements of atomic defect distribution near a solid surface. Defects are produced by argon-ion bombardment of an Al(110) surface in ultrahigh vacuum. Defect profiles have a typical width of 15–25 Å and contain a broader tail extending to 50–100 Å. The defect density at the outermost atomic layers saturates at high argon fluences to a few atomic percent, depending on sputtering conditions. Defect production rate at >1 keV Ar+ energies is typically 1–5 vacancy-interstitial pairs per incident ion. Molecular-dynamics simulations of the collision cascade predict similar defect distributions. Peer reviewed